<?xml version="1.0" encoding="utf-8"?>
<!--XBRL document created with Toppan Merrill Bridge  11.2.0.5 -->
<!--Based on XBRL 2.1-->
<!--Created on: 3/12/2026 10:21:18 AM-->
<!--Modified on: 3/12/2026 10:21:18 AM-->
<link:linkbase xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xlink="http://www.w3.org/1999/xlink">
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DocumentDocumentAndEntityInformation" roleURI="http://www.proqr.com/role/DocumentDocumentAndEntityInformation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#StatementConsolidatedStatementOfFinancialPosition" roleURI="http://www.proqr.com/role/StatementConsolidatedStatementOfFinancialPosition" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#StatementConsolidatedStatementOfProfitOrLossAndComprehensiveIncome" roleURI="http://www.proqr.com/role/StatementConsolidatedStatementOfProfitOrLossAndComprehensiveIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#StatementConsolidatedStatementOfChangesInEquity" roleURI="http://www.proqr.com/role/StatementConsolidatedStatementOfChangesInEquity" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#StatementConsolidatedStatementOfCashFlows" roleURI="http://www.proqr.com/role/StatementConsolidatedStatementOfCashFlows" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureGeneralInformation" roleURI="http://www.proqr.com/role/DisclosureGeneralInformation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBasisOfPreparation" roleURI="http://www.proqr.com/role/DisclosureBasisOfPreparation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSignificantAccountingPolicies" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPolicies" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureNewStandardsAndInterpretationsNotYetAdopted" roleURI="http://www.proqr.com/role/DisclosureNewStandardsAndInterpretationsNotYetAdopted" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialRiskManagement" roleURI="http://www.proqr.com/role/DisclosureFinancialRiskManagement" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSegmentInformation" roleURI="http://www.proqr.com/role/DisclosureSegmentInformation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosurePropertyPlantAndEquipment" roleURI="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipment" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureInvestmentsInFinancialAssets" roleURI="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssets" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherTaxes" roleURI="http://www.proqr.com/role/DisclosureOtherTaxes" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureTradeAndOtherReceivables" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCashAndCashEquivalents" roleURI="http://www.proqr.com/role/DisclosureCashAndCashEquivalents" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquity" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquity" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBorrowings" roleURI="http://www.proqr.com/role/DisclosureBorrowings" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureDeferredIncome" roleURI="http://www.proqr.com/role/DisclosureDeferredIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherCurrentLiabilities" roleURI="http://www.proqr.com/role/DisclosureOtherCurrentLiabilities" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRevenue" roleURI="http://www.proqr.com/role/DisclosureRevenue" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherIncome" roleURI="http://www.proqr.com/role/DisclosureOtherIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOperatingCosts" roleURI="http://www.proqr.com/role/DisclosureOperatingCosts" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEmployeeBenefits" roleURI="http://www.proqr.com/role/DisclosureEmployeeBenefits" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialIncomeAndExpense" roleURI="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpense" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss" roleURI="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureIncomeTaxes" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxes" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEarningsPerShare" roleURI="http://www.proqr.com/role/DisclosureEarningsPerShare" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureLeases" roleURI="http://www.proqr.com/role/DisclosureLeases" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCommitmentsAndContingencies" roleURI="http://www.proqr.com/role/DisclosureCommitmentsAndContingencies" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRelatedPartyTransactions" roleURI="http://www.proqr.com/role/DisclosureRelatedPartyTransactions" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureAuditorFees" roleURI="http://www.proqr.com/role/DisclosureAuditorFees" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSubsequentEvents" roleURI="http://www.proqr.com/role/DisclosureSubsequentEvents" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSignificantAccountingPoliciesPolicies" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesPolicies" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSignificantAccountingPoliciesTables" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialRiskManagementTables" roleURI="http://www.proqr.com/role/DisclosureFinancialRiskManagementTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosurePropertyPlantAndEquipmentTables" roleURI="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherTaxesTables" roleURI="http://www.proqr.com/role/DisclosureOtherTaxesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureTradeAndOtherReceivablesTables" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCashAndCashEquivalentsTables" roleURI="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityTables" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBorrowingsTables" roleURI="http://www.proqr.com/role/DisclosureBorrowingsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureDeferredIncomeTables" roleURI="http://www.proqr.com/role/DisclosureDeferredIncomeTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRevenueTables" roleURI="http://www.proqr.com/role/DisclosureRevenueTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherIncomeTables" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOperatingCostsTables" roleURI="http://www.proqr.com/role/DisclosureOperatingCostsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEmployeeBenefitsTables" roleURI="http://www.proqr.com/role/DisclosureEmployeeBenefitsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialIncomeAndExpenseTables" roleURI="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpenseTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTables" roleURI="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureIncomeTaxesTables" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEarningsPerShareTables" roleURI="http://www.proqr.com/role/DisclosureEarningsPerShareTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureLeasesTables" roleURI="http://www.proqr.com/role/DisclosureLeasesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRelatedPartyTransactionsTables" roleURI="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureAuditorFeesTables" roleURI="http://www.proqr.com/role/DisclosureAuditorFeesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureGeneralInformationDetails" roleURI="http://www.proqr.com/role/DisclosureGeneralInformationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBasisOfPreparationDetails" roleURI="http://www.proqr.com/role/DisclosureBasisOfPreparationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSignificantAccountingPoliciesDetails" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSignificantAccountingPoliciesEstimatedUsefulLivesDetails" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesEstimatedUsefulLivesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialRiskManagementNarrativeDetails" roleURI="http://www.proqr.com/role/DisclosureFinancialRiskManagementNarrativeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialRiskManagementUndiscountedLiabilitiesByMaturityDetails" roleURI="http://www.proqr.com/role/DisclosureFinancialRiskManagementUndiscountedLiabilitiesByMaturityDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureSegmentInformationDetails" roleURI="http://www.proqr.com/role/DisclosureSegmentInformationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosurePropertyPlantAndEquipmentDetails" roleURI="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureInvestmentsInFinancialAssetsDetails" roleURI="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssetsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherTaxesDetails" roleURI="http://www.proqr.com/role/DisclosureOtherTaxesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureTradeAndOtherReceivablesDetails" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCashAndCashEquivalentsDetails" roleURI="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityShareCapitalDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityShareCapitalDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquitySaleOfSharesDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquitySaleOfSharesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityShareOptionsDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityShareOptionsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityShareOptionsAndRestrictedStockUnitsDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityShareOptionsAndRestrictedStockUnitsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityMovementsInNumberOfOptionsOutstandingDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityMovementsInNumberOfOptionsOutstandingDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureShareholdersEquityMovementsInNumberOfRsusOutstandingDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityMovementsInNumberOfRsusOutstandingDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBorrowingsDetails" roleURI="http://www.proqr.com/role/DisclosureBorrowingsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureBorrowingsReconciliationOfMovementsOfLiabilitiesToCashFlowsArisingFromFinancingActivitiesDetails" roleURI="http://www.proqr.com/role/DisclosureBorrowingsReconciliationOfMovementsOfLiabilitiesToCashFlowsArisingFromFinancingActivitiesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureDeferredIncomeSummaryOfDeferredIncomeDetails" roleURI="http://www.proqr.com/role/DisclosureDeferredIncomeSummaryOfDeferredIncomeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureDeferredIncomeSummaryOfDeferredIncomeUndiscountedDeferredIncomeByMaturityDetails" roleURI="http://www.proqr.com/role/DisclosureDeferredIncomeSummaryOfDeferredIncomeUndiscountedDeferredIncomeByMaturityDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherCurrentLiabiltiesDetails" roleURI="http://www.proqr.com/role/DisclosureOtherCurrentLiabiltiesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRevenueSummaryOfRevenueRecognizedDetails" roleURI="http://www.proqr.com/role/DisclosureRevenueSummaryOfRevenueRecognizedDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRevenueSummaryOfChangesInCurrentAndNonCurrentDeferredRevenueDetails" roleURI="http://www.proqr.com/role/DisclosureRevenueSummaryOfChangesInCurrentAndNonCurrentDeferredRevenueDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRevenueAdditionalInformationDetails" roleURI="http://www.proqr.com/role/DisclosureRevenueAdditionalInformationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherIncomeDetails" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOtherIncomeNarrativeDetails" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeNarrativeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureOperatingCostsDetails" roleURI="http://www.proqr.com/role/DisclosureOperatingCostsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEmployeeBenefitsDetails" roleURI="http://www.proqr.com/role/DisclosureEmployeeBenefitsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureFinancialIncomeAndExpenseDetails" roleURI="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpenseDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossDetails" roleURI="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureIncomeTaxesDetails" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureIncomeTaxesDeferredTaxDetails" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxesDeferredTaxDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureEarningsPerShareDetails" roleURI="http://www.proqr.com/role/DisclosureEarningsPerShareDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureLeasesDetails" roleURI="http://www.proqr.com/role/DisclosureLeasesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCommitmentsAndContingenciesClaimsAndPatentLicenseAgreementDetails" roleURI="http://www.proqr.com/role/DisclosureCommitmentsAndContingenciesClaimsAndPatentLicenseAgreementDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureCommitmentsAndContingenciesClinicalSupportAgreementsDetails" roleURI="http://www.proqr.com/role/DisclosureCommitmentsAndContingenciesClinicalSupportAgreementsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRelatedPartyTransactionsCompensationDetails" roleURI="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsCompensationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureRelatedPartyTransactionsStockOptionsDetails" roleURI="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsStockOptionsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20251231.xsd#DisclosureAuditorFeesDetails" roleURI="http://www.proqr.com/role/DisclosureAuditorFeesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2025/ecd-2025.xsd#InsiderTradingPoliciesProc" roleURI="http://xbrl.sec.gov/ecd/role/InsiderTradingPoliciesProc" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="https://xbrl.sec.gov/cyd/2025/cyd-2025.xsd#CybersecurityRiskManagementAndStrategyDisclosure" roleURI="http://xbrl.sec.gov/cyd/role/CybersecurityRiskManagementAndStrategyDisclosure" xmlns="http://www.xbrl.org/2003/linkbase" />
  <link:roleRef roleURI="http://www.xbrl.org/2009/role/negatedLabel" xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedLabel" />
  <link:roleRef roleURI="http://www.xbrl.org/2009/role/negatedTerseLabel" xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedTerseLabel" />
  <link:roleRef roleURI="http://www.xbrl.org/2009/role/negatedTotalLabel" xlink:type="simple" xlink:href="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd#negatedTotalLabel" />
  <presentationLink xlink:role="http://www.proqr.com/role/DocumentDocumentAndEntityInformation" xlink:type="extended" xlink:title="995200090 - Document - Document and Entity Information" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DocumentAndEntityInformationAbstract" xlink:label="DocumentAndEntityInformationAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStatementTable" xlink:label="prqr_IfrsStatementTable_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="prqr_IfrsStatementTable_639089076753397657" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressesAddressTypeAxis" xlink:label="dei_EntityAddressesAddressTypeAxis_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementTable_639089076753397657" xlink:to="dei_EntityAddressesAddressTypeAxis_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AddressTypeDomain" xlink:label="dei_AddressTypeDomain_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_EntityAddressesAddressTypeAxis_639089076753397657" xlink:to="dei_AddressTypeDomain_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_BusinessContactMember" xlink:label="dei_BusinessContactMember_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="dei_AddressTypeDomain_639089076753397657" xlink:to="dei_BusinessContactMember_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStatementLineItems" xlink:label="prqr_IfrsStatementLineItems_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementTable_639089076753397657" xlink:to="prqr_IfrsStatementLineItems_639089076753397657" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentType" xlink:label="dei_DocumentType_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentType_639089076753397657" order="1" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentRegistrationStatement" xlink:label="dei_DocumentRegistrationStatement_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentRegistrationStatement_639089076753397657" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentAnnualReport" xlink:label="dei_DocumentAnnualReport_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentAnnualReport_639089076753397657" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentPeriodEndDate" xlink:label="dei_DocumentPeriodEndDate_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentPeriodEndDate_639089076753397657" order="4" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CurrentFiscalYearEndDate" xlink:label="dei_CurrentFiscalYearEndDate_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_CurrentFiscalYearEndDate_639089076753397657" order="5" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentTransitionReport" xlink:label="dei_DocumentTransitionReport_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentTransitionReport_639089076753397657" order="6" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentShellCompanyReport" xlink:label="dei_DocumentShellCompanyReport_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentShellCompanyReport_639089076753397657" order="7" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityFileNumber" xlink:label="dei_EntityFileNumber_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityFileNumber_639089076753397657" order="8" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityRegistrantName" xlink:label="dei_EntityRegistrantName_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityRegistrantName_639089076753397657" order="9" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityIncorporationStateCountryCode" xlink:label="dei_EntityIncorporationStateCountryCode_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityIncorporationStateCountryCode_639089076753397657" order="10" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressAddressLine1" xlink:label="dei_EntityAddressAddressLine1_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityAddressAddressLine1_639089076753397657" order="11" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressCityOrTown" xlink:label="dei_EntityAddressCityOrTown_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityAddressCityOrTown_639089076753397657" order="12" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressPostalZipCode" xlink:label="dei_EntityAddressPostalZipCode_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityAddressPostalZipCode_639089076753397657" order="13" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CityAreaCode" xlink:label="dei_CityAreaCode_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_CityAreaCode_639089076753397657" order="14" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_LocalPhoneNumber" xlink:label="dei_LocalPhoneNumber_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_LocalPhoneNumber_639089076753397657" order="15" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_ContactPersonnelName" xlink:label="dei_ContactPersonnelName_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_ContactPersonnelName_639089076753397657" order="16" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityAddressCountry" xlink:label="dei_EntityAddressCountry_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityAddressCountry_639089076753397657" order="17" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_ContactPersonnelEmailAddress" xlink:label="dei_ContactPersonnelEmailAddress_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_ContactPersonnelEmailAddress_639089076753397657" order="18" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_Security12bTitle" xlink:label="dei_Security12bTitle_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_Security12bTitle_639089076753397657" order="19" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_TradingSymbol" xlink:label="dei_TradingSymbol_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_TradingSymbol_639089076753397657" order="20" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_SecurityExchangeName" xlink:label="dei_SecurityExchangeName_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_SecurityExchangeName_639089076753397657" order="21" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCommonStockSharesOutstanding" xlink:label="dei_EntityCommonStockSharesOutstanding_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityCommonStockSharesOutstanding_639089076753397657" order="22" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityWellKnownSeasonedIssuer" xlink:label="dei_EntityWellKnownSeasonedIssuer_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityWellKnownSeasonedIssuer_639089076753397657" order="23" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityVoluntaryFilers" xlink:label="dei_EntityVoluntaryFilers_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityVoluntaryFilers_639089076753397657" order="24" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCurrentReportingStatus" xlink:label="dei_EntityCurrentReportingStatus_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityCurrentReportingStatus_639089076753397657" order="25" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityInteractiveDataCurrent" xlink:label="dei_EntityInteractiveDataCurrent_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityInteractiveDataCurrent_639089076753397657" order="26" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityFilerCategory" xlink:label="dei_EntityFilerCategory_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityFilerCategory_639089076753397657" order="27" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityEmergingGrowthCompany" xlink:label="dei_EntityEmergingGrowthCompany_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityEmergingGrowthCompany_639089076753397657" order="28" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_IcfrAuditorAttestationFlag" xlink:label="dei_IcfrAuditorAttestationFlag_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_IcfrAuditorAttestationFlag_639089076753397657" order="29" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentAccountingStandard" xlink:label="dei_DocumentAccountingStandard_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentAccountingStandard_639089076753397657" order="30" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityShellCompany" xlink:label="dei_EntityShellCompany_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityShellCompany_639089076753397657" order="31" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentFiscalYearFocus" xlink:label="dei_DocumentFiscalYearFocus_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentFiscalYearFocus_639089076753397657" order="32" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentFiscalPeriodFocus" xlink:label="dei_DocumentFiscalPeriodFocus_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentFiscalPeriodFocus_639089076753397657" order="33" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCentralIndexKey" xlink:label="dei_EntityCentralIndexKey_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_EntityCentralIndexKey_639089076753397657" order="34" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AmendmentFlag" xlink:label="dei_AmendmentFlag_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_AmendmentFlag_639089076753397657" order="35" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AuditorFirmId" xlink:label="dei_AuditorFirmId_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_AuditorFirmId_639089076753397657" order="36" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AuditorName" xlink:label="dei_AuditorName_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_AuditorName_639089076753397657" order="37" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AuditorLocation" xlink:label="dei_AuditorLocation_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_AuditorLocation_639089076753397657" order="38" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentFinStmtErrorCorrectionFlag" xlink:label="dei_DocumentFinStmtErrorCorrectionFlag_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsStatementLineItems_639089076753397657" xlink:to="dei_DocumentFinStmtErrorCorrectionFlag_639089076753397657" order="39" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementConsolidatedStatementOfFinancialPosition" xlink:type="extended" xlink:title="995200100 - Statement - Consolidated Statement of Financial Position" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfFinancialPositionAbstract" xlink:label="StatementOfFinancialPositionAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AssetsAbstract" xlink:label="ifrs-full_AssetsAbstract_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfFinancialPositionAbstract" xlink:to="ifrs-full_AssetsAbstract_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome" xlink:label="ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncurrentAssets" xlink:label="ifrs-full_NoncurrentAssets_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_NoncurrentAssets_639089076753397657" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="7" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax" xlink:label="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639089076753397657" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherCurrentReceivables" xlink:label="ifrs-full_TradeAndOtherCurrentReceivables_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_TradeAndOtherCurrentReceivables_639089076753397657" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_CashAndCashEquivalents_639089076753397657" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentAssets" xlink:label="ifrs-full_CurrentAssets_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_CurrentAssets_639089076753397657" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="8" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Assets" xlink:label="ifrs-full_Assets_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639089076753397657" xlink:to="ifrs-full_Assets_639089076753397657" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityAndLiabilitiesAbstract" xlink:label="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfFinancialPositionAbstract" xlink:to="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityAbstract" xlink:label="ifrs-full_EquityAbstract_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_EquityAbstract_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IssuedCapital" xlink:label="ifrs-full_IssuedCapital_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_IssuedCapital_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SharePremium" xlink:label="ifrs-full_SharePremium_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_SharePremium_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherReserves" xlink:label="ifrs-full_OtherReserves_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_OtherReserves_639089076753397657" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RetainedEarnings" xlink:label="ifrs-full_RetainedEarnings_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_RetainedEarnings_639089076753397657" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityAttributableToOwnersOfParent" xlink:label="ifrs-full_EquityAttributableToOwnersOfParent_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_EquityAttributableToOwnersOfParent_639089076753397657" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="8" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Equity" xlink:label="ifrs-full_Equity_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639089076753397657" xlink:to="ifrs-full_Equity_639089076753397657" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LiabilitiesAbstract" xlink:label="ifrs-full_LiabilitiesAbstract_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_LiabilitiesAbstract_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncurrentLeaseLiabilities" xlink:label="ifrs-full_NoncurrentLeaseLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_NoncurrentLeaseLiabilities_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities" xlink:label="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncurrentLiabilities" xlink:label="ifrs-full_NoncurrentLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_NoncurrentLiabilities_639089076753397657" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings" xlink:label="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639089076753397657" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentLeaseLiabilities" xlink:label="ifrs-full_CurrentLeaseLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentLeaseLiabilities_639089076753397657" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentDerivativeFinancialLiabilities" xlink:label="ifrs-full_CurrentDerivativeFinancialLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentDerivativeFinancialLiabilities_639089076753397657" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherCurrentPayables" xlink:label="ifrs-full_TradeAndOtherCurrentPayables_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_TradeAndOtherCurrentPayables_639089076753397657" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="8" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentPayablesOnSocialSecurityAndTaxesOtherThanIncomeTax" xlink:label="ifrs-full_CurrentPayablesOnSocialSecurityAndTaxesOtherThanIncomeTax_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentPayablesOnSocialSecurityAndTaxesOtherThanIncomeTax_639089076753397657" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities" xlink:label="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639089076753397657" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherCurrentLiabilities" xlink:label="ifrs-full_OtherCurrentLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_OtherCurrentLiabilities_639089076753397657" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentLiabilities" xlink:label="ifrs-full_CurrentLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_CurrentLiabilities_639089076753397657" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="8" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Liabilities" xlink:label="ifrs-full_Liabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_Liabilities_639089076753397657" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityAndLiabilities" xlink:label="ifrs-full_EquityAndLiabilities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639089076753397657" xlink:to="ifrs-full_EquityAndLiabilities_639089076753397657" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="5" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementConsolidatedStatementOfProfitOrLossAndComprehensiveIncome" xlink:type="extended" xlink:title="995200200 - Statement - Consolidated Statement of Profit or Loss and Comprehensive Income" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfComprehensiveIncomeAbstract" xlink:label="StatementOfComprehensiveIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueFromContractsWithCustomers" xlink:label="ifrs-full_RevenueFromContractsWithCustomers_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_RevenueFromContractsWithCustomers_639089076753397657" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherIncome" xlink:label="ifrs-full_OtherIncome_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OtherIncome_639089076753397657" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ResearchAndDevelopmentExpense" xlink:label="ifrs-full_ResearchAndDevelopmentExpense_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ResearchAndDevelopmentExpense_639089076753397657" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GeneralAndAdministrativeExpense" xlink:label="ifrs-full_GeneralAndAdministrativeExpense_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GeneralAndAdministrativeExpense_639089076753397657" order="4" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OperatingExpense" xlink:label="ifrs-full_OperatingExpense_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OperatingExpense_639089076753397657" order="5" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedTotalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossFromOperatingActivities" xlink:label="ifrs-full_ProfitLossFromOperatingActivities_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossFromOperatingActivities_639089076753397657" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinanceIncome" xlink:label="ifrs-full_FinanceIncome_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_FinanceIncome_639089076753397657" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinanceCosts" xlink:label="ifrs-full_FinanceCosts_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_FinanceCosts_639089076753397657" order="8" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GainLossOnSaleOfAssociates" xlink:label="prqr_GainLossOnSaleOfAssociates_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="prqr_GainLossOnSaleOfAssociates_639089076753397657" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainsLossesRecognisedWhenControlInSubsidiaryIsLost" xlink:label="ifrs-full_GainsLossesRecognisedWhenControlInSubsidiaryIsLost_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GainsLossesRecognisedWhenControlInSubsidiaryIsLost_639089076753397657" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid" xlink:label="ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid_639089076753397657" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid_639089076753397657" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss" xlink:label="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639089076753527974" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossBeforeTax" xlink:label="ifrs-full_ProfitLossBeforeTax_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossBeforeTax_639089076753527974" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncomeTaxExpenseContinuingOperations" xlink:label="ifrs-full_IncomeTaxExpenseContinuingOperations_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_IncomeTaxExpenseContinuingOperations_639089076753527974" order="14" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLoss_639089076753527974" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherComprehensiveIncomeAbstract" xlink:label="ifrs-full_OtherComprehensiveIncomeAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OtherComprehensiveIncomeAbstract_639089076753527974" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillNotBeReclassifiedToProfitOrLossNetOfTaxAbstract" xlink:label="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillNotBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_OtherComprehensiveIncomeAbstract_639089076753527974" xlink:to="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillNotBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments" xlink:label="ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillNotBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" xlink:to="ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillBeReclassifiedToProfitOrLossNetOfTaxAbstract" xlink:label="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_OtherComprehensiveIncomeAbstract_639089076753527974" xlink:to="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation" xlink:label="ifrs-full_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfOtherComprehensiveIncomeThatWillBeReclassifiedToProfitOrLossNetOfTaxAbstract_639089076753527974" xlink:to="ifrs-full_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComprehensiveIncome" xlink:label="ifrs-full_ComprehensiveIncome_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_OtherComprehensiveIncomeAbstract_639089076753527974" xlink:to="ifrs-full_ComprehensiveIncome_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossAttributableToAbstract" xlink:label="ifrs-full_ProfitLossAttributableToAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossAttributableToAbstract_639089076753527974" order="17" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossAttributableToOwnersOfParent" xlink:label="ifrs-full_ProfitLossAttributableToOwnersOfParent_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProfitLossAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ProfitLossAttributableToOwnersOfParent_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossAttributableToNoncontrollingInterests" xlink:label="ifrs-full_ProfitLossAttributableToNoncontrollingInterests_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProfitLossAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ProfitLossAttributableToNoncontrollingInterests_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_6390890767535279741" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProfitLossAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ProfitLoss_6390890767535279741" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComprehensiveIncomeAttributableToAbstract" xlink:label="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639089076753527974" order="18" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComprehensiveIncomeAttributableToOwnersOfParent" xlink:label="ifrs-full_ComprehensiveIncomeAttributableToOwnersOfParent_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ComprehensiveIncomeAttributableToOwnersOfParent_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComprehensiveIncomeAttributableToNoncontrollingInterests" xlink:label="ifrs-full_ComprehensiveIncomeAttributableToNoncontrollingInterests_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ComprehensiveIncomeAttributableToNoncontrollingInterests_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComprehensiveIncome" xlink:label="ifrs-full_ComprehensiveIncome_6390890767535279741" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639089076753527974" xlink:to="ifrs-full_ComprehensiveIncome_6390890767535279741" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract" xlink:label="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639089076753527974" order="19" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageShares" xlink:label="ifrs-full_WeightedAverageShares_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639089076753527974" xlink:to="ifrs-full_WeightedAverageShares_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustedWeightedAverageShares" xlink:label="ifrs-full_AdjustedWeightedAverageShares_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639089076753527974" xlink:to="ifrs-full_AdjustedWeightedAverageShares_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EarningsPerShareAbstract" xlink:label="ifrs-full_EarningsPerShareAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_EarningsPerShareAbstract_639089076753527974" order="20" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BasicEarningsLossPerShare" xlink:label="ifrs-full_BasicEarningsLossPerShare_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EarningsPerShareAbstract_639089076753527974" xlink:to="ifrs-full_BasicEarningsLossPerShare_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DilutedEarningsLossPerShare" xlink:label="ifrs-full_DilutedEarningsLossPerShare_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EarningsPerShareAbstract_639089076753527974" xlink:to="ifrs-full_DilutedEarningsLossPerShare_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementConsolidatedStatementOfChangesInEquity" xlink:type="extended" xlink:title="995200300 - Statement - Consolidated Statement of Changes in Equity" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfChangesInEquityAbstract" xlink:label="StatementOfChangesInEquityAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfChangesInEquityTable" xlink:label="ifrs-full_StatementOfChangesInEquityTable_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfChangesInEquityAbstract" xlink:to="ifrs-full_StatementOfChangesInEquityTable_639089076753527974" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComponentsOfEquityAxis" xlink:label="ifrs-full_ComponentsOfEquityAxis_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityTable_639089076753527974" xlink:to="ifrs-full_ComponentsOfEquityAxis_639089076753527974" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityAttributableToOwnersOfParentMember" xlink:label="ifrs-full_EquityAttributableToOwnersOfParentMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_EquityAttributableToOwnersOfParentMember_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IssuedCapitalMember" xlink:label="ifrs-full_IssuedCapitalMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_IssuedCapitalMember_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SharePremiumMember" xlink:label="ifrs-full_SharePremiumMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_SharePremiumMember_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ReserveOfSharebasedPaymentsMember" xlink:label="ifrs-full_ReserveOfSharebasedPaymentsMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_ReserveOfSharebasedPaymentsMember_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ReserveOfExchangeDifferencesOnTranslationMember" xlink:label="ifrs-full_ReserveOfExchangeDifferencesOnTranslationMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_ReserveOfExchangeDifferencesOnTranslationMember_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RetainedEarningsMember" xlink:label="ifrs-full_RetainedEarningsMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_RetainedEarningsMember_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncontrollingInterestsMember" xlink:label="ifrs-full_NoncontrollingInterestsMember_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_NoncontrollingInterestsMember_639089076753527974" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ComponentsOfEquityDomain" xlink:label="ifrs-full_ComponentsOfEquityDomain_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639089076753527974" xlink:to="ifrs-full_ComponentsOfEquityDomain_639089076753527974" order="8" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfChangesInEquityLineItems" xlink:label="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityTable_639089076753527974" xlink:to="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Equity" xlink:label="ifrs-full_Equity_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_Equity_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_ProfitLoss_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherComprehensiveIncome" xlink:label="ifrs-full_OtherComprehensiveIncome_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_OtherComprehensiveIncome_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncreaseDecreaseThroughSharebasedPaymentTransactions" xlink:label="ifrs-full_IncreaseDecreaseThroughSharebasedPaymentTransactions_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_IncreaseDecreaseThroughSharebasedPaymentTransactions_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IssueOfEquity" xlink:label="ifrs-full_IssueOfEquity_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_IssueOfEquity_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="7" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SharesOptionsLapsed" xlink:label="prqr_SharesOptionsLapsed_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="prqr_SharesOptionsLapsed_639089076753527974" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncreaseDecreaseThroughExerciseOfOptions" xlink:label="ifrs-full_IncreaseDecreaseThroughExerciseOfOptions_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_IncreaseDecreaseThroughExerciseOfOptions_639089076753527974" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Equity" xlink:label="ifrs-full_Equity_6390890767535279741" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639089076753527974" xlink:to="ifrs-full_Equity_6390890767535279741" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="9" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementConsolidatedStatementOfCashFlows" xlink:type="extended" xlink:title="995200400 - Statement - Consolidated Statement of Cash Flows" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_StatementOfCashFlowsAbstract" xlink:label="StatementOfCashFlowsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract" xlink:label="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProfitLoss_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForReconcileProfitLossAbstract" xlink:label="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdjustmentsForOtherIncome" xlink:label="prqr_AdjustmentsForOtherIncome_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="prqr_AdjustmentsForOtherIncome_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForDepreciationExpense" xlink:label="ifrs-full_AdjustmentsForDepreciationExpense_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForDepreciationExpense_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdjustmentsForGainsLossesOnDerecognitionOfSubsidiaries" xlink:label="prqr_AdjustmentsForGainsLossesOnDerecognitionOfSubsidiaries_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="prqr_AdjustmentsForGainsLossesOnDerecognitionOfSubsidiaries_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForSharebasedPayments" xlink:label="ifrs-full_AdjustmentsForSharebasedPayments_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForSharebasedPayments_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForFinanceIncomeCost" xlink:label="ifrs-full_AdjustmentsForFinanceIncomeCost_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForFinanceIncomeCost_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdjustmentsForGainsLossesOnDerecognitionOfFinancialLiabilities" xlink:label="prqr_AdjustmentsForGainsLossesOnDerecognitionOfFinancialLiabilities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="prqr_AdjustmentsForGainsLossesOnDerecognitionOfFinancialLiabilities_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForIncreaseDecreaseInFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss" xlink:label="ifrs-full_AdjustmentsForIncreaseDecreaseInFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForIncreaseDecreaseInFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss_639089076753527974" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForIncomeTaxExpense" xlink:label="ifrs-full_AdjustmentsForIncomeTaxExpense_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForIncomeTaxExpense_639089076753527974" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustmentsForIncreaseDecreaseInDeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_AdjustmentsForIncreaseDecreaseInDeferredIncomeIncludingContractLiabilities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_AdjustmentsForIncreaseDecreaseInDeferredIncomeIncludingContractLiabilities_639089076753527974" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdjustmentsForOtherChangesInWorkingCapital" xlink:label="prqr_AdjustmentsForOtherChangesInWorkingCapital_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="prqr_AdjustmentsForOtherChangesInWorkingCapital_639089076753527974" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInOperations" xlink:label="ifrs-full_CashFlowsFromUsedInOperations_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_CashFlowsFromUsedInOperations_639089076753527974" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncomeTaxesPaidRefundClassifiedAsOperatingActivities" xlink:label="ifrs-full_IncomeTaxesPaidRefundClassifiedAsOperatingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_IncomeTaxesPaidRefundClassifiedAsOperatingActivities_639089076753527974" order="12" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestReceivedClassifiedAsOperatingActivities" xlink:label="ifrs-full_InterestReceivedClassifiedAsOperatingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_InterestReceivedClassifiedAsOperatingActivities_639089076753527974" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestPaidClassifiedAsOperatingActivities" xlink:label="ifrs-full_InterestPaidClassifiedAsOperatingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_InterestPaidClassifiedAsOperatingActivities_639089076753527974" order="14" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInOperatingActivities" xlink:label="ifrs-full_CashFlowsFromUsedInOperatingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639089076753527974" xlink:to="ifrs-full_CashFlowsFromUsedInOperatingActivities_639089076753527974" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract" xlink:label="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities" xlink:label="ifrs-full_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromSalesOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities" xlink:label="ifrs-full_ProceedsFromSalesOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromSalesOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities" xlink:label="ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CashOutflowsFromTransactionCostsOnSaleOfIntellectualProperty" xlink:label="prqr_CashOutflowsFromTransactionCostsOnSaleOfIntellectualProperty_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="prqr_CashOutflowsFromTransactionCostsOnSaleOfIntellectualProperty_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PurchaseOfFinancialInstrumentsClassifiedAsInvestingActivities" xlink:label="ifrs-full_PurchaseOfFinancialInstrumentsClassifiedAsInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_PurchaseOfFinancialInstrumentsClassifiedAsInvestingActivities_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromSalesOrMaturityOfFinancialInstrumentsClassifiedAsInvestingActivities" xlink:label="ifrs-full_ProceedsFromSalesOrMaturityOfFinancialInstrumentsClassifiedAsInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromSalesOrMaturityOfFinancialInstrumentsClassifiedAsInvestingActivities_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInInvestingActivities" xlink:label="ifrs-full_CashFlowsFromUsedInInvestingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_CashFlowsFromUsedInInvestingActivities_639089076753527974" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract" xlink:label="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromIssuingShares" xlink:label="ifrs-full_ProceedsFromIssuingShares_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromIssuingShares_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromExerciseOfOptions" xlink:label="ifrs-full_ProceedsFromExerciseOfOptions_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromExerciseOfOptions_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities" xlink:label="ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RepaymentsOfConvertibleLoans" xlink:label="prqr_RepaymentsOfConvertibleLoans_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="prqr_RepaymentsOfConvertibleLoans_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities" xlink:label="ifrs-full_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashFlowsFromUsedInFinancingActivities" xlink:label="ifrs-full_CashFlowsFromUsedInFinancingActivities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639089076753527974" xlink:to="ifrs-full_CashFlowsFromUsedInFinancingActivities_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges" xlink:label="ifrs-full_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EffectOfExchangeRateChangesOnCashAndCashEquivalents" xlink:label="ifrs-full_EffectOfExchangeRateChangesOnCashAndCashEquivalents_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_EffectOfExchangeRateChangesOnCashAndCashEquivalents_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashAndCashEquivalents_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_6390890767535279741" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashAndCashEquivalents_6390890767535279741" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureGeneralInformation" xlink:type="extended" xlink:title="995210101 - Disclosure - General Information" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GeneralInformationAbstract" xlink:label="GeneralInformationAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfGeneralInformationExplanatory" xlink:label="prqr_DisclosureOfGeneralInformationExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="GeneralInformationAbstract" xlink:to="prqr_DisclosureOfGeneralInformationExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBasisOfPreparation" xlink:type="extended" xlink:title="995210201 - Disclosure - Basis of Preparation" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_BasisOfPreparationAbstract" xlink:label="BasisOfPreparationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfBasisOfPreparationOfFinancialStatementsExplanatory" xlink:label="ifrs-full_DisclosureOfBasisOfPreparationOfFinancialStatementsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasisOfPreparationAbstract" xlink:to="ifrs-full_DisclosureOfBasisOfPreparationOfFinancialStatementsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPolicies" xlink:type="extended" xlink:title="995210301 - Disclosure - Significant Accounting Policies" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfMaterialAccountingPolicyInformationExplanatory" xlink:label="ifrs-full_DisclosureOfMaterialAccountingPolicyInformationExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DisclosureOfMaterialAccountingPolicyInformationExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureNewStandardsAndInterpretationsNotYetAdopted" xlink:type="extended" xlink:title="995210401 - Disclosure - New standards and interpretations not yet adopted" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfExpectedImpactOfInitialApplicationOfNewStandardsOrInterpretationsAbstract" xlink:label="DescriptionOfExpectedImpactOfInitialApplicationOfNewStandardsOrInterpretationsAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ExplanationOfNewStandardsOrInterpretationsNotApplied" xlink:label="prqr_ExplanationOfNewStandardsOrInterpretationsNotApplied_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DescriptionOfExpectedImpactOfInitialApplicationOfNewStandardsOrInterpretationsAbstract" xlink:to="prqr_ExplanationOfNewStandardsOrInterpretationsNotApplied_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialRiskManagement" xlink:type="extended" xlink:title="995210501 - Disclosure - Financial Risk Management" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:label="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinancialRiskManagementExplanatory" xlink:label="ifrs-full_DisclosureOfFinancialRiskManagementExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:to="ifrs-full_DisclosureOfFinancialRiskManagementExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSegmentInformation" xlink:type="extended" xlink:title="995210601 - Disclosure - Segment Information" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfOperatingSegmentsAbstract" xlink:label="DisclosureOfOperatingSegmentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfEntitysReportableSegmentsExplanatory" xlink:label="ifrs-full_DisclosureOfEntitysReportableSegmentsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfOperatingSegmentsAbstract" xlink:to="ifrs-full_DisclosureOfEntitysReportableSegmentsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipment" xlink:type="extended" xlink:title="995210701 - Disclosure - Property, Plant and Equipment" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:label="DisclosureOfPropertyPlantAndEquipmentAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentExplanatory" xlink:label="ifrs-full_DisclosureOfPropertyPlantAndEquipmentExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssets" xlink:type="extended" xlink:title="995210801 - Disclosure - Investments in Financial Assets" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_InvestmentsInFinancialAssetsAbstract" xlink:label="prqr_InvestmentsInFinancialAssetsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinancialAssetsExplanatory" xlink:label="ifrs-full_DisclosureOfFinancialAssetsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_InvestmentsInFinancialAssetsAbstract" xlink:to="ifrs-full_DisclosureOfFinancialAssetsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherTaxes" xlink:type="extended" xlink:title="995210901 - Disclosure - Other Taxes" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SocialSecurityAndOtherTaxesAbstract" xlink:label="SocialSecurityAndOtherTaxesAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfSocialSecurityAndOtherTaxesExplanatory" xlink:label="prqr_DisclosureOfSocialSecurityAndOtherTaxesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SocialSecurityAndOtherTaxesAbstract" xlink:to="prqr_DisclosureOfSocialSecurityAndOtherTaxesExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivables" xlink:type="extended" xlink:title="995211001 - Disclosure - Trade and Other Receivables" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherReceivablesAbstract" xlink:label="ifrs-full_TradeAndOtherReceivablesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTradeAndOtherReceivablesExplanatory" xlink:label="ifrs-full_DisclosureOfTradeAndOtherReceivablesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract" xlink:to="ifrs-full_DisclosureOfTradeAndOtherReceivablesExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCashAndCashEquivalents" xlink:type="extended" xlink:title="995211101 - Disclosure - Cash and Cash Equivalents" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalentsAbstract" xlink:label="CashAndCashEquivalentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfCashAndCashEquivalentsExplanatory" xlink:label="ifrs-full_DisclosureOfCashAndCashEquivalentsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_DisclosureOfCashAndCashEquivalentsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquity" xlink:type="extended" xlink:title="995211201 - Disclosure - Shareholders' Equity" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfShareCapitalReservesAndOtherEquityInterestExplanatory" xlink:label="ifrs-full_DisclosureOfShareCapitalReservesAndOtherEquityInterestExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfShareCapitalReservesAndOtherEquityInterestExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowings" xlink:type="extended" xlink:title="995211301 - Disclosure - Borrowings" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsAbstract" xlink:label="BorrowingsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfBorrowingsExplanatory" xlink:label="ifrs-full_DisclosureOfBorrowingsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfBorrowingsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncome" xlink:type="extended" xlink:title="995211401 - Disclosure - Deferred Income" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDeferredIncomeExplanatory" xlink:label="ifrs-full_DisclosureOfDeferredIncomeExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract" xlink:to="ifrs-full_DisclosureOfDeferredIncomeExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherCurrentLiabilities" xlink:type="extended" xlink:title="995211501 - Disclosure - Other Current Liabilities" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OtherCurrentLiabilitiesAbstract" xlink:label="prqr_OtherCurrentLiabilitiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfOtherCurrentLiabilitiesExplanatory" xlink:label="ifrs-full_DisclosureOfOtherCurrentLiabilitiesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherCurrentLiabilitiesAbstract" xlink:to="ifrs-full_DisclosureOfOtherCurrentLiabilitiesExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenue" xlink:type="extended" xlink:title="995211601 - Disclosure - Revenue" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueAbstract" xlink:label="ifrs-full_RevenueAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfRevenueExplanatory" xlink:label="ifrs-full_DisclosureOfRevenueExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract" xlink:to="ifrs-full_DisclosureOfRevenueExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherIncome" xlink:type="extended" xlink:title="995211701 - Disclosure - Other Income" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfOtherOperatingIncomeExplanatory" xlink:label="ifrs-full_DisclosureOfOtherOperatingIncomeExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="ifrs-full_DisclosureOfOtherOperatingIncomeExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOperatingCosts" xlink:type="extended" xlink:title="995211801 - Disclosure - Operating Costs" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseByNatureAbstract" xlink:label="ifrs-full_ExpenseByNatureAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfExpensesByNatureExplanatory" xlink:label="ifrs-full_DisclosureOfExpensesByNatureExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract" xlink:to="ifrs-full_DisclosureOfExpensesByNatureExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEmployeeBenefits" xlink:type="extended" xlink:title="995211901 - Disclosure - Employee Benefits" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDefinedBenefitPlansAbstract" xlink:label="DisclosureOfDefinedBenefitPlansAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfEmployeeBenefitsExplanatory" xlink:label="ifrs-full_DisclosureOfEmployeeBenefitsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfDefinedBenefitPlansAbstract" xlink:to="ifrs-full_DisclosureOfEmployeeBenefitsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpense" xlink:type="extended" xlink:title="995212001 - Disclosure - Financial Income and Expense" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:label="DisclosureOfFinancialIncomeAndExpenseAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinanceIncomeExpenseExplanatory" xlink:label="ifrs-full_DisclosureOfFinanceIncomeExpenseExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_DisclosureOfFinanceIncomeExpenseExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLoss" xlink:type="extended" xlink:title="995212101 - Disclosure - Results related to financial liabilities measured at fair value through profit or loss" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" xlink:label="FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinancialInstrumentsAtFairValueThroughProfitOrLossExplanatory" xlink:label="ifrs-full_DisclosureOfFinancialInstrumentsAtFairValueThroughProfitOrLossExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" xlink:to="ifrs-full_DisclosureOfFinancialInstrumentsAtFairValueThroughProfitOrLossExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxes" xlink:type="extended" xlink:title="995212201 - Disclosure - Income Taxes" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" xlink:label="MajorComponentsOfTaxExpenseIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfIncomeTaxExplanatory" xlink:label="ifrs-full_DisclosureOfIncomeTaxExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="MajorComponentsOfTaxExpenseIncomeAbstract" xlink:to="ifrs-full_DisclosureOfIncomeTaxExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEarningsPerShare" xlink:type="extended" xlink:title="995212301 - Disclosure - Earnings Per Share" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EarningsPerShareAbstract" xlink:label="EarningsPerShareAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfEarningsPerShareExplanatory" xlink:label="ifrs-full_DisclosureOfEarningsPerShareExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_DisclosureOfEarningsPerShareExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureLeases" xlink:type="extended" xlink:title="995212401 - Disclosure - Leases" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PresentationOfLeasesForLesseeAbstract" xlink:label="PresentationOfLeasesForLesseeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfLeasesExplanatory" xlink:label="ifrs-full_DisclosureOfLeasesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="PresentationOfLeasesForLesseeAbstract" xlink:to="ifrs-full_DisclosureOfLeasesExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCommitmentsAndContingencies" xlink:type="extended" xlink:title="995212501 - Disclosure - Commitments and Contingencies" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesAbstract" xlink:label="DisclosureOfContingentLiabilitiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfCommitmentsAndContingentLiabilitiesExplanatory" xlink:label="ifrs-full_DisclosureOfCommitmentsAndContingentLiabilitiesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfContingentLiabilitiesAbstract" xlink:to="ifrs-full_DisclosureOfCommitmentsAndContingentLiabilitiesExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRelatedPartyTransactions" xlink:type="extended" xlink:title="995212601 - Disclosure - Related-Party Transactions" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:label="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfRelatedPartyExplanatory" xlink:label="ifrs-full_DisclosureOfRelatedPartyExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:to="ifrs-full_DisclosureOfRelatedPartyExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureAuditorFees" xlink:type="extended" xlink:title="995212701 - Disclosure - Auditor fees" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AuditorsRemunerationAbstract" xlink:label="AuditorsRemunerationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfAuditorsRemunerationExplanatory" xlink:label="ifrs-full_DisclosureOfAuditorsRemunerationExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="AuditorsRemunerationAbstract" xlink:to="ifrs-full_DisclosureOfAuditorsRemunerationExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSubsequentEvents" xlink:type="extended" xlink:title="995212801 - Disclosure - Subsequent events" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNonadjustingEventsAfterReportingPeriodAbstract" xlink:label="DisclosureOfNonadjustingEventsAfterReportingPeriodAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfEventsAfterReportingPeriodExplanatory" xlink:label="ifrs-full_DisclosureOfEventsAfterReportingPeriodExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNonadjustingEventsAfterReportingPeriodAbstract" xlink:to="ifrs-full_DisclosureOfEventsAfterReportingPeriodExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesPolicies" xlink:type="extended" xlink:title="99920302 - Disclosure - Significant Accounting Policies (Policies)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfBasisOfConsolidationExplanatory" xlink:label="ifrs-full_DisclosureOfBasisOfConsolidationExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DisclosureOfBasisOfConsolidationExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForFinancialInstrumentsExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForFinancialInstrumentsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForFinancialInstrumentsExplanatory_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForForeignCurrencyTranslationExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForForeignCurrencyTranslationExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForForeignCurrencyTranslationExplanatory_639089076753527974" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForRecognitionOfRevenue" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForRecognitionOfRevenue_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForRecognitionOfRevenue_639089076753527974" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DescriptionOfAccountingPolicyForRecognitionOfOtherIncomeTextBlock" xlink:label="prqr_DescriptionOfAccountingPolicyForRecognitionOfOtherIncomeTextBlock_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="prqr_DescriptionOfAccountingPolicyForRecognitionOfOtherIncomeTextBlock_639089076753527974" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForGovernmentGrants" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForGovernmentGrants_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForGovernmentGrants_639089076753527974" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForEmployeeBenefitsExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForEmployeeBenefitsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForEmployeeBenefitsExplanatory_639089076753527974" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForIncomeTaxExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForIncomeTaxExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForIncomeTaxExplanatory_639089076753527974" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForPropertyPlantAndEquipmentExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForPropertyPlantAndEquipmentExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForPropertyPlantAndEquipmentExplanatory_639089076753527974" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForIntangibleAssetsOtherThanGoodwillExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForIntangibleAssetsOtherThanGoodwillExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForIntangibleAssetsOtherThanGoodwillExplanatory_639089076753527974" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForImpairmentOfAssetsExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForImpairmentOfAssetsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForImpairmentOfAssetsExplanatory_639089076753527974" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForFinancialAssetsExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForFinancialAssetsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForFinancialAssetsExplanatory_639089076753527974" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyToDetermineComponentsOfCashAndCashEquivalents" xlink:label="ifrs-full_DescriptionOfAccountingPolicyToDetermineComponentsOfCashAndCashEquivalents_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyToDetermineComponentsOfCashAndCashEquivalents_639089076753527974" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForFinancialLiabilitiesExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForFinancialLiabilitiesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForFinancialLiabilitiesExplanatory_639089076753527974" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForLeasesExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForLeasesExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForLeasesExplanatory_639089076753527974" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfAccountingPolicyForNoncurrentAssetsOrDisposalGroupsClassifiedAsHeldForSaleExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForNoncurrentAssetsOrDisposalGroupsClassifiedAsHeldForSaleExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForNoncurrentAssetsOrDisposalGroupsClassifiedAsHeldForSaleExplanatory_639089076753527974" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesTables" xlink:type="extended" xlink:title="99930303 - Disclosure - Significant Accounting Policies (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfUsefulLivesPropertyPlantAndEquipmentExplanatory" xlink:label="prqr_ScheduleOfUsefulLivesPropertyPlantAndEquipmentExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="prqr_ScheduleOfUsefulLivesPropertyPlantAndEquipmentExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialRiskManagementTables" xlink:type="extended" xlink:title="99930503 - Disclosure - Financial Risk Management (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:label="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityAnalysisForNonderivativeFinancialLiabilities" xlink:label="ifrs-full_MaturityAnalysisForNonderivativeFinancialLiabilities_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:to="ifrs-full_MaturityAnalysisForNonderivativeFinancialLiabilities_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFairValueMeasurementExplanatory" xlink:label="ifrs-full_DisclosureOfFairValueMeasurementExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:to="ifrs-full_DisclosureOfFairValueMeasurementExplanatory_639089076753527974" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentTables" xlink:type="extended" xlink:title="99930703 - Disclosure - Property, Plant and Equipment (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:label="DisclosureOfPropertyPlantAndEquipmentAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfReconciliationOfChangesInPropertyPlantAndEquipmentIncludingRightofuseAssetsExplanatory" xlink:label="ifrs-full_DisclosureOfReconciliationOfChangesInPropertyPlantAndEquipmentIncludingRightofuseAssetsExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:to="ifrs-full_DisclosureOfReconciliationOfChangesInPropertyPlantAndEquipmentIncludingRightofuseAssetsExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherTaxesTables" xlink:type="extended" xlink:title="99930903 - Disclosure - Other Taxes (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SocialSecurityAndOtherTaxesAbstract" xlink:label="SocialSecurityAndOtherTaxesAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SocialSecurityAndOtherTaxesTableTextBlock" xlink:label="prqr_SocialSecurityAndOtherTaxesTableTextBlock_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SocialSecurityAndOtherTaxesAbstract" xlink:to="prqr_SocialSecurityAndOtherTaxesTableTextBlock_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesTables" xlink:type="extended" xlink:title="99931003 - Disclosure - Trade and Other Receivables (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherReceivablesAbstract" xlink:label="ifrs-full_TradeAndOtherReceivablesAbstract_1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock" xlink:label="prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_1" xlink:to="prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsTables" xlink:type="extended" xlink:title="99931103 - Disclosure - Cash and Cash Equivalents (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalentsAbstract" xlink:label="CashAndCashEquivalentsAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsScheduleOfCashAndCashEquivalentsTableTextBlock" xlink:label="prqr_IfrsScheduleOfCashAndCashEquivalentsTableTextBlock_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="prqr_IfrsScheduleOfCashAndCashEquivalentsTableTextBlock_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityTables" xlink:type="extended" xlink:title="99931203 - Disclosure - Shareholders' Equity (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalExplanatory" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalExplanatory_639089076753527974" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalExplanatory_639089076753527974" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfIndirectMeasurementOfFairValueOfGoodsOrServicesReceivedShareOptionsGrantedDuringPeriodExplanatory" xlink:label="ifrs-full_DisclosureOfIndirectMeasurementOfFairValueOfGoodsOrServicesReceivedShareOptionsGrantedDuringPeriodExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfIndirectMeasurementOfFairValueOfGoodsOrServicesReceivedShareOptionsGrantedDuringPeriodExplanatory_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfShareOptionsExplanatory" xlink:label="ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfShareOptionsExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfShareOptionsExplanatory_639089076753684688" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfOtherEquityInstrumentsExplanatory" xlink:label="ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfOtherEquityInstrumentsExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfNumberAndWeightedAverageExercisePricesOfOtherEquityInstrumentsExplanatory_639089076753684688" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowingsTables" xlink:type="extended" xlink:title="99931303 - Disclosure - Borrowings (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsAbstract" xlink:label="BorrowingsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsExplanatory" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfReconciliationOfLiabilitiesArisingFromFinancingActivitiesExplanatory" xlink:label="ifrs-full_DisclosureOfReconciliationOfLiabilitiesArisingFromFinancingActivitiesExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfReconciliationOfLiabilitiesArisingFromFinancingActivitiesExplanatory_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncomeTables" xlink:type="extended" xlink:title="99931403 - Disclosure - Deferred Income (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract_1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfDeferredIncomeTableTextBlock" xlink:label="prqr_ScheduleOfDeferredIncomeTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_1" xlink:to="prqr_ScheduleOfDeferredIncomeTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfUndiscountedDeferredIncomeByMaturityTableTextBlock" xlink:label="prqr_ScheduleOfUndiscountedDeferredIncomeByMaturityTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_1" xlink:to="prqr_ScheduleOfUndiscountedDeferredIncomeByMaturityTableTextBlock_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenueTables" xlink:type="extended" xlink:title="99931603 - Disclosure - Revenue (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueAbstract" xlink:label="RevenueAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfRevenueFromContractsWithCustomersExplanatory" xlink:label="ifrs-full_DisclosureOfRevenueFromContractsWithCustomersExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="RevenueAbstract" xlink:to="ifrs-full_DisclosureOfRevenueFromContractsWithCustomersExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersExplanatory" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="RevenueAbstract" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersExplanatory_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherIncomeTables" xlink:type="extended" xlink:title="99931703 - Disclosure - Other Income (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory" xlink:label="prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOperatingCostsTables" xlink:type="extended" xlink:title="99931803 - Disclosure - Operating Costs (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseByNatureAbstract" xlink:label="ifrs-full_ExpenseByNatureAbstract_2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfExpensesExplanatory" xlink:label="ifrs-full_DisclosureOfExpensesExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_2" xlink:to="ifrs-full_DisclosureOfExpensesExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEmployeeBenefitsTables" xlink:type="extended" xlink:title="99931903 - Disclosure - Employee Benefits (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDefinedBenefitPlansAbstract" xlink:label="DisclosureOfDefinedBenefitPlansAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfEmployeeBenefitsExpenseTableTextBlock" xlink:label="prqr_DisclosureOfEmployeeBenefitsExpenseTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfDefinedBenefitPlansAbstract" xlink:to="prqr_DisclosureOfEmployeeBenefitsExpenseTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfEmployeePerActivityTableTextBlock" xlink:label="prqr_DisclosureOfEmployeePerActivityTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfDefinedBenefitPlansAbstract" xlink:to="prqr_DisclosureOfEmployeePerActivityTableTextBlock_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpenseTables" xlink:type="extended" xlink:title="99932003 - Disclosure - Financial Income and Expense (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:label="DisclosureOfFinancialIncomeAndExpenseAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfFinancialIncomeAndExpenseTableTextBlock" xlink:label="prqr_ScheduleOfFinancialIncomeAndExpenseTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="prqr_ScheduleOfFinancialIncomeAndExpenseTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTables" xlink:type="extended" xlink:title="99932103 - Disclosure - Results related to financial liabilities measured at fair value through profit or loss (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" xlink:label="FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract_1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTableTextBlock" xlink:label="prqr_DisclosureOfFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract_1" xlink:to="prqr_DisclosureOfFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxesTables" xlink:type="extended" xlink:title="99932203 - Disclosure - Income Taxes (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" xlink:label="MajorComponentsOfTaxExpenseIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfEffectiveIncomeTaxRateReconciliationsTableTextBlock" xlink:label="prqr_ScheduleOfEffectiveIncomeTaxRateReconciliationsTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="MajorComponentsOfTaxExpenseIncomeAbstract" xlink:to="prqr_ScheduleOfEffectiveIncomeTaxRateReconciliationsTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEarningsPerShareTables" xlink:type="extended" xlink:title="99932303 - Disclosure - Earnings Per Share (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EarningsPerShareAbstract" xlink:label="EarningsPerShareAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EarningsPerShareExplanatory" xlink:label="ifrs-full_EarningsPerShareExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_EarningsPerShareExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureLeasesTables" xlink:type="extended" xlink:title="99932403 - Disclosure - Leases (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PresentationOfLeasesForLesseeAbstract" xlink:label="PresentationOfLeasesForLesseeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsExplanatory" xlink:label="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="PresentationOfLeasesForLesseeAbstract" xlink:to="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsTables" xlink:type="extended" xlink:title="99932603 - Disclosure - Related-Party Transactions (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:label="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfInformationAboutKeyManagementPersonnelExplanatory" xlink:label="ifrs-full_DisclosureOfInformationAboutKeyManagementPersonnelExplanatory_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:to="ifrs-full_DisclosureOfInformationAboutKeyManagementPersonnelExplanatory_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureAuditorFeesTables" xlink:type="extended" xlink:title="99932703 - Disclosure - Auditor fees (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AuditorsRemunerationAbstract" xlink:label="AuditorsRemunerationAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScheduleOfAuditorsRemunerationForServicesProvidedTableTextBlock" xlink:label="prqr_ScheduleOfAuditorsRemunerationForServicesProvidedTableTextBlock_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="AuditorsRemunerationAbstract" xlink:to="prqr_ScheduleOfAuditorsRemunerationForServicesProvidedTableTextBlock_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureGeneralInformationDetails" xlink:type="extended" xlink:title="99940101 - Disclosure - General Information (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GeneralInformationAbstract" xlink:label="GeneralInformationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable" xlink:label="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="GeneralInformationAbstract" xlink:to="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639089076753684688" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInSubsidiariesAxis" xlink:label="ifrs-full_SignificantInvestmentsInSubsidiariesAxis_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639089076753684688" xlink:to="ifrs-full_SignificantInvestmentsInSubsidiariesAxis_639089076753684688" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInSubsidiariesDomain" xlink:label="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesAxis_639089076753684688" xlink:to="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsHoldingB.v.Member" xlink:label="prqr_ProqrTherapeuticsHoldingB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsHoldingB.v.Member_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIB.v.Member" xlink:label="prqr_ProqrTherapeuticsIB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIB.v.Member_639089076753684688" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIiB.v.Member" xlink:label="prqr_ProqrTherapeuticsIiB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIiB.v.Member_639089076753684688" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIiiB.v.Member" xlink:label="prqr_ProqrTherapeuticsIiiB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIiiB.v.Member_639089076753684688" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIvB.v.Member" xlink:label="prqr_ProqrTherapeuticsIvB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIvB.v.Member_639089076753684688" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsVB.v.Member" xlink:label="prqr_ProqrTherapeuticsVB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsVB.v.Member_639089076753684688" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsViB.v.Member" xlink:label="prqr_ProqrTherapeuticsViB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsViB.v.Member_639089076753684688" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsViiB.v.Member" xlink:label="prqr_ProqrTherapeuticsViiB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsViiB.v.Member_639089076753684688" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsViiiB.v.Member" xlink:label="prqr_ProqrTherapeuticsViiiB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsViiiB.v.Member_639089076753684688" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIxB.v.Member" xlink:label="prqr_ProqrTherapeuticsIxB.v.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIxB.v.Member_639089076753684688" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProqrTherapeuticsIInc.Member" xlink:label="prqr_ProqrTherapeuticsIInc.Member_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639089076753684688" xlink:to="prqr_ProqrTherapeuticsIInc.Member_639089076753684688" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesAxis" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639089076753684688" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753684688" order="2" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesDomain" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753684688" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753684688" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_YarrowBiotechnologyMember" xlink:label="prqr_YarrowBiotechnologyMember_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753684688" xlink:to="prqr_YarrowBiotechnologyMember_639089076753684688" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems" xlink:label="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639089076753684688" xlink:to="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639089076753684688" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProportionOfOwnershipInterestInSubsidiary" xlink:label="ifrs-full_ProportionOfOwnershipInterestInSubsidiary_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639089076753684688" xlink:to="ifrs-full_ProportionOfOwnershipInterestInSubsidiary_639089076753684688" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProportionOfOwnershipInterestInAssociate" xlink:label="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639089076753684688" xlink:to="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753684688" order="2" use="optional" priority="2" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBasisOfPreparationDetails" xlink:type="extended" xlink:title="99940201 - Disclosure - Basis of Preparation (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_BasisOfPreparationAbstract" xlink:label="BasisOfPreparationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsTable" xlink:label="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsTable_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BasisOfPreparationAbstract" xlink:to="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsTable_639089076753684688" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsTable_639089076753684688" xlink:to="ifrs-full_CounterpartiesAxis_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753684688" xlink:to="ifrs-full_CounterpartiesDomain_639089076753684688" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639089076753684688" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753684688" xlink:to="prqr_EliLillyAndCompanyMember_639089076753684688" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsLineItems" xlink:label="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsTable_639089076753684688" xlink:to="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsLineItems_639089076753840967" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfInitialApplicationOfStandardsOrInterpretationsLineItems_639089076753840967" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesDetails" xlink:type="extended" xlink:title="99940301 - Disclosure - Significant Accounting Policies (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076753840967" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076753840967" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_UnusedTaxLossesMember" xlink:label="ifrs-full_UnusedTaxLossesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076753840967" xlink:to="ifrs-full_UnusedTaxLossesMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsNumberOfReportableSegments" xlink:label="prqr_IfrsNumberOfReportableSegments_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" xlink:to="prqr_IfrsNumberOfReportableSegments_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredTaxAssets" xlink:label="ifrs-full_DeferredTaxAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" xlink:to="ifrs-full_DeferredTaxAssets_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfPerformanceObligationsInCollaborationAndLicenseAgreements" xlink:label="prqr_NumberOfPerformanceObligationsInCollaborationAndLicenseAgreements_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" xlink:to="prqr_NumberOfPerformanceObligationsInCollaborationAndLicenseAgreements_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfPerformanceObligationsInResearchAndCollaborationAgreements" xlink:label="prqr_NumberOfPerformanceObligationsInResearchAndCollaborationAgreements_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076753840967" xlink:to="prqr_NumberOfPerformanceObligationsInResearchAndCollaborationAgreements_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesEstimatedUsefulLivesDetails" xlink:type="extended" xlink:title="99940302 - Disclosure - Significant Accounting Policies - Estimated useful lives (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable" xlink:label="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" order="1" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LeaseholdImprovementsMember" xlink:label="ifrs-full_LeaseholdImprovementsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="ifrs-full_LeaseholdImprovementsMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LaboratoryEquipmentMember" xlink:label="prqr_LaboratoryEquipmentMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="prqr_LaboratoryEquipmentMember_639089076753840967" order="2" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherPropertyPlantAndEquipmentMember" xlink:label="ifrs-full_OtherPropertyPlantAndEquipmentMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="ifrs-full_OtherPropertyPlantAndEquipmentMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_RangeAxis_639089076753840967" order="2" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076753840967" xlink:to="ifrs-full_RangeDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BottomOfRangeMember" xlink:label="ifrs-full_BottomOfRangeMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753840967" xlink:to="ifrs-full_BottomOfRangeMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753840967" xlink:to="ifrs-full_TopOfRangeMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentLineItems" xlink:label="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentLineItems_639089076753840967" order="3" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_UsefulLifeMeasuredAsPeriodOfTimePropertyPlantAndEquipment" xlink:label="ifrs-full_UsefulLifeMeasuredAsPeriodOfTimePropertyPlantAndEquipment_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfDetailedInformationAboutIntangiblesPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_UsefulLifeMeasuredAsPeriodOfTimePropertyPlantAndEquipment_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialRiskManagementNarrativeDetails" xlink:type="extended" xlink:title="99940501 - Disclosure - Financial Risk Management - Narrative (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:label="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfInterestRatesAxis" xlink:label="ifrs-full_TypesOfInterestRatesAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_TypesOfInterestRatesAxis_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfInterestRatesDomain" xlink:label="ifrs-full_TypesOfInterestRatesDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfInterestRatesAxis_639089076753840967" xlink:to="ifrs-full_TypesOfInterestRatesDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FixedInterestRateMember" xlink:label="ifrs-full_FixedInterestRateMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfInterestRatesDomain_639089076753840967" xlink:to="ifrs-full_FixedInterestRateMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PastDueStatusAxis" xlink:label="ifrs-full_PastDueStatusAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_PastDueStatusAxis_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PastDueStatusDomain" xlink:label="ifrs-full_PastDueStatusDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_PastDueStatusAxis_639089076753840967" xlink:to="ifrs-full_PastDueStatusDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PastDueOrImpairedMember" xlink:label="prqr_PastDueOrImpairedMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_PastDueStatusDomain_639089076753840967" xlink:to="prqr_PastDueOrImpairedMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2025/elts/srt-2025.xsd#srt_CurrencyAxis" xlink:label="srt_CurrencyAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="srt_CurrencyAxis_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/currency/2025/currency-2025.xsd#currency_AllCurrenciesDomain" xlink:label="currency_AllCurrenciesDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_CurrencyAxis_639089076753840967" xlink:to="currency_AllCurrenciesDomain_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/currency/2025/currency-2025.xsd#currency_USD" xlink:label="currency_USD_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="currency_AllCurrenciesDomain_639089076753840967" xlink:to="currency_USD_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfRisksAxis" xlink:label="ifrs-full_TypesOfRisksAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_TypesOfRisksAxis_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfRisksDomain" xlink:label="ifrs-full_TypesOfRisksDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfRisksAxis_639089076753840967" xlink:to="ifrs-full_TypesOfRisksDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrencyRiskMember" xlink:label="ifrs-full_CurrencyRiskMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfRisksDomain_639089076753840967" xlink:to="ifrs-full_CurrencyRiskMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestRateRiskMember" xlink:label="ifrs-full_InterestRateRiskMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfRisksDomain_639089076753840967" xlink:to="ifrs-full_InterestRateRiskMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NetAssetsLiabilities" xlink:label="ifrs-full_NetAssetsLiabilities_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="ifrs-full_NetAssetsLiabilities_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMinimumTerm" xlink:label="prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMinimumTerm_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMinimumTerm_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMaximumTerm" xlink:label="prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMaximumTerm_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_ForeignCurrencyDenominatedReceivablesAndTradePayableMaximumTerm_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfReasonablyPossibleWeakeningOfForeignCurrency" xlink:label="prqr_PercentageOfReasonablyPossibleWeakeningOfForeignCurrency_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_PercentageOfReasonablyPossibleWeakeningOfForeignCurrency_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInProfitLossFromReasonablyPossibleWeakeningInForeignCurrency" xlink:label="prqr_IncreaseDecreaseInProfitLossFromReasonablyPossibleWeakeningInForeignCurrency_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseInProfitLossFromReasonablyPossibleWeakeningInForeignCurrency_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfReasonablyPossibleStrengtheningOfForeignCurrency" xlink:label="prqr_PercentageOfReasonablyPossibleStrengtheningOfForeignCurrency_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_PercentageOfReasonablyPossibleStrengtheningOfForeignCurrency_639089076753840967" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Borrowings" xlink:label="ifrs-full_Borrowings_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="ifrs-full_Borrowings_639089076753840967" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfLargeInstitutionsAtWhichSubstantiallyAllEntitySCashAndCashEquivalentsAreHeld" xlink:label="prqr_NumberOfLargeInstitutionsAtWhichSubstantiallyAllEntitySCashAndCashEquivalentsAreHeld_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_NumberOfLargeInstitutionsAtWhichSubstantiallyAllEntitySCashAndCashEquivalentsAreHeld_639089076753840967" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinancialAssets" xlink:label="ifrs-full_FinancialAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="ifrs-full_FinancialAssets_639089076753840967" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CreditLimitsExceededDuringReportingPeriod" xlink:label="prqr_CreditLimitsExceededDuringReportingPeriod_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_CreditLimitsExceededDuringReportingPeriod_639089076753840967" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfReasonablyPossibleIncreaseOrDecreaseInInterestRates" xlink:label="prqr_PercentageOfReasonablyPossibleIncreaseOrDecreaseInInterestRates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_PercentageOfReasonablyPossibleIncreaseOrDecreaseInInterestRates_639089076753840967" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfReasonablyPossibleIncreaseInInterestRates" xlink:label="prqr_PercentageOfReasonablyPossibleIncreaseInInterestRates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_PercentageOfReasonablyPossibleIncreaseInInterestRates_639089076753840967" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleIncreaseInInterestRates" xlink:label="prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleIncreaseInInterestRates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleIncreaseInInterestRates_639089076753840967" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfReasonablyPossibleDecreaseInInterestRates" xlink:label="prqr_PercentageOfReasonablyPossibleDecreaseInInterestRates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_PercentageOfReasonablyPossibleDecreaseInInterestRates_639089076753840967" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleDecreaseInInterestRates" xlink:label="prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleDecreaseInInterestRates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseInProfitLossBeforeTaxDueToReasonablyPossibleDecreaseInInterestRates_639089076753840967" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialRiskManagementUndiscountedLiabilitiesByMaturityDetails" xlink:type="extended" xlink:title="99940502 - Disclosure - Financial Risk Management - Undiscounted Liabilities by Maturity (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:label="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNatureAndExtentOfRisksArisingFromFinancialInstrumentsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialLiabilitiesAxis" xlink:label="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialLiabilitiesDomain" xlink:label="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076753840967" xlink:to="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LongtermBorrowingsMember" xlink:label="ifrs-full_LongtermBorrowingsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076753840967" xlink:to="ifrs-full_LongtermBorrowingsMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LeaseLiabilitiesMember" xlink:label="ifrs-full_LeaseLiabilitiesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076753840967" xlink:to="ifrs-full_LeaseLiabilitiesMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TradePayablesAndOtherPayablesMember" xlink:label="prqr_TradePayablesAndOtherPayablesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076753840967" xlink:to="prqr_TradePayablesAndOtherPayablesMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityAxis" xlink:label="ifrs-full_MaturityAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_MaturityAxis_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityDomain" xlink:label="ifrs-full_MaturityDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityAxis_639089076753840967" xlink:to="ifrs-full_MaturityDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NotLaterThanOneYearMember" xlink:label="ifrs-full_NotLaterThanOneYearMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753840967" xlink:to="ifrs-full_NotLaterThanOneYearMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember" xlink:label="ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753840967" xlink:to="ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember" xlink:label="ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753840967" xlink:to="ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LaterThanFiveYearsMember" xlink:label="ifrs-full_LaterThanFiveYearsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753840967" xlink:to="ifrs-full_LaterThanFiveYearsMember_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" order="3" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NonderivativeFinancialLiabilitiesUndiscountedCashFlows" xlink:label="ifrs-full_NonderivativeFinancialLiabilitiesUndiscountedCashFlows_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753840967" xlink:to="ifrs-full_NonderivativeFinancialLiabilitiesUndiscountedCashFlows_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSegmentInformationDetails" xlink:type="extended" xlink:title="99940601 - Disclosure - Segment Information (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfOperatingSegmentsAbstract" xlink:label="DisclosureOfOperatingSegmentsAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsNumberOfReportableSegments" xlink:label="prqr_IfrsNumberOfReportableSegments_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfOperatingSegmentsAbstract" xlink:to="prqr_IfrsNumberOfReportableSegments_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentDetails" xlink:type="extended" xlink:title="99940701 - Disclosure - Property, Plant and Equipment (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:label="DisclosureOfPropertyPlantAndEquipmentAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable" xlink:label="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CarryingAmountAccumulatedDepreciationAmortisationAndImpairmentAndGrossCarryingAmountAxis" xlink:label="ifrs-full_CarryingAmountAccumulatedDepreciationAmortisationAndImpairmentAndGrossCarryingAmountAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_CarryingAmountAccumulatedDepreciationAmortisationAndImpairmentAndGrossCarryingAmountAxis_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CarryingAmountMember" xlink:label="ifrs-full_CarryingAmountMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CarryingAmountAccumulatedDepreciationAmortisationAndImpairmentAndGrossCarryingAmountAxis_639089076753840967" xlink:to="ifrs-full_CarryingAmountMember_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GrossCarryingAmountMember" xlink:label="ifrs-full_GrossCarryingAmountMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CarryingAmountMember_639089076753840967" xlink:to="ifrs-full_GrossCarryingAmountMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AccumulatedDepreciationAmortisationAndImpairmentMember" xlink:label="ifrs-full_AccumulatedDepreciationAmortisationAndImpairmentMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CarryingAmountMember_639089076753840967" xlink:to="ifrs-full_AccumulatedDepreciationAmortisationAndImpairmentMember_639089076753840967" order="2" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AccumulatedDepreciationAndAmortisationMember" xlink:label="ifrs-full_AccumulatedDepreciationAndAmortisationMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AccumulatedDepreciationAmortisationAndImpairmentMember_639089076753840967" xlink:to="ifrs-full_AccumulatedDepreciationAndAmortisationMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076753840967" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LeaseholdImprovementsMember" xlink:label="ifrs-full_LeaseholdImprovementsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="ifrs-full_LeaseholdImprovementsMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LaboratoryEquipmentMember" xlink:label="prqr_LaboratoryEquipmentMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="prqr_LaboratoryEquipmentMember_639089076753840967" order="2" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherPropertyPlantAndEquipmentMember" xlink:label="ifrs-full_OtherPropertyPlantAndEquipmentMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076753840967" xlink:to="ifrs-full_OtherPropertyPlantAndEquipmentMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" order="3" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" order="1" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsResearchAndDevelopmentExpenseMember" xlink:label="prqr_IfrsResearchAndDevelopmentExpenseMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" xlink:to="prqr_IfrsResearchAndDevelopmentExpenseMember_639089076753840967" order="1" use="optional" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsSellingGeneralAndAdministrativeExpensesMember" xlink:label="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" xlink:to="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems" xlink:label="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdditionsOtherThanThroughBusinessCombinationsPropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_AdditionsOtherThanThroughBusinessCombinationsPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_AdditionsOtherThanThroughBusinessCombinationsPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DepreciationPropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_DepreciationPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_DepreciationPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseThroughLeaseModificationsPropertyPlantAndEquipment" xlink:label="prqr_IncreaseDecreaseThroughLeaseModificationsPropertyPlantAndEquipment_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseThroughLeaseModificationsPropertyPlantAndEquipment_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncreaseDecreaseInPropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_IncreaseDecreaseInPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_IncreaseDecreaseInPropertyPlantAndEquipmentIncludingRightofuseAssets_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets" xlink:label="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_6390890767538409671" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_6390890767538409671" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RightofuseAssets" xlink:label="ifrs-full_RightofuseAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639089076753840967" xlink:to="ifrs-full_RightofuseAssets_639089076753840967" order="7" use="optional" priority="2" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssetsDetails" xlink:type="extended" xlink:title="99940801 - Disclosure - Investments in Financial Assets (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_InvestmentsInFinancialAssetsAbstract" xlink:label="prqr_InvestmentsInFinancialAssetsAbstract_3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable" xlink:label="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_InvestmentsInFinancialAssetsAbstract_3" xlink:to="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesAxis" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639089076753840967" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesDomain" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753840967" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_YarrowBiotechnologyMember" xlink:label="prqr_YarrowBiotechnologyMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753840967" xlink:to="prqr_YarrowBiotechnologyMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WingsTherapeuticsIncMember" xlink:label="prqr_WingsTherapeuticsIncMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753840967" xlink:to="prqr_WingsTherapeuticsIncMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialAssetsAxis" xlink:label="ifrs-full_ClassesOfFinancialAssetsAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639089076753840967" xlink:to="ifrs-full_ClassesOfFinancialAssetsAxis_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialAssetsDomain" xlink:label="ifrs-full_ClassesOfFinancialAssetsDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialAssetsAxis_639089076753840967" xlink:to="ifrs-full_ClassesOfFinancialAssetsDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EquityInvestmentsMember" xlink:label="ifrs-full_EquityInvestmentsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialAssetsDomain_639089076753840967" xlink:to="ifrs-full_EquityInvestmentsMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_YarrowBiotechnologyMember" xlink:label="prqr_YarrowBiotechnologyMember_6390890767538409671" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityInvestmentsMember_639089076753840967" xlink:to="prqr_YarrowBiotechnologyMember_6390890767538409671" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PhoenicisTherapeuticsIncMember" xlink:label="prqr_PhoenicisTherapeuticsIncMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityInvestmentsMember_639089076753840967" xlink:to="prqr_PhoenicisTherapeuticsIncMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems" xlink:label="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639089076753840967" xlink:to="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProportionOfOwnershipInterestInAssociate" xlink:label="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfDirectorsOnBoardThatEntityHasRightToAppoint" xlink:label="prqr_NumberOfDirectorsOnBoardThatEntityHasRightToAppoint_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="prqr_NumberOfDirectorsOnBoardThatEntityHasRightToAppoint_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TotalNumberOfDirectorsOnBoard" xlink:label="prqr_TotalNumberOfDirectorsOnBoard_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="prqr_TotalNumberOfDirectorsOnBoard_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ProportionOfOwnershipInterest" xlink:label="prqr_ProportionOfOwnershipInterest_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="prqr_ProportionOfOwnershipInterest_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome" xlink:label="ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="ifrs-full_FairValueOfInvestmentsInEquityInstrumentsDesignatedAsMeasuredAtFairValueThroughOtherComprehensiveIncome_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments" xlink:label="ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="ifrs-full_OtherComprehensiveIncomeNetOfTaxGainsLossesFromInvestmentsInEquityInstruments_639089076753840967" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GainLossOnSaleOfAssociates" xlink:label="prqr_GainLossOnSaleOfAssociates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639089076753840967" xlink:to="prqr_GainLossOnSaleOfAssociates_639089076753840967" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherTaxesDetails" xlink:type="extended" xlink:title="99940901 - Disclosure - Other Taxes (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SocialSecurityAndOtherTaxesAbstract" xlink:label="SocialSecurityAndOtherTaxesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentValueAddedTaxReceivables" xlink:label="ifrs-full_CurrentValueAddedTaxReceivables_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SocialSecurityAndOtherTaxesAbstract" xlink:to="ifrs-full_CurrentValueAddedTaxReceivables_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CurrentWageTaxReceivable" xlink:label="prqr_CurrentWageTaxReceivable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SocialSecurityAndOtherTaxesAbstract" xlink:to="prqr_CurrentWageTaxReceivable_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax" xlink:label="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SocialSecurityAndOtherTaxesAbstract" xlink:to="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesDetails" xlink:type="extended" xlink:title="99941001 - Disclosure - Trade and Other Receivables (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherReceivablesAbstract" xlink:label="ifrs-full_TradeAndOtherReceivablesAbstract_2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CurrentReceivablesFromCollaborationAgreements" xlink:label="prqr_CurrentReceivablesFromCollaborationAgreements_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="prqr_CurrentReceivablesFromCollaborationAgreements_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentPrepayments" xlink:label="ifrs-full_CurrentPrepayments_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="ifrs-full_CurrentPrepayments_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentAccruedIncomeIncludingCurrentContractAssets" xlink:label="ifrs-full_CurrentAccruedIncomeIncludingCurrentContractAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="ifrs-full_CurrentAccruedIncomeIncludingCurrentContractAssets_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherCurrentReceivables" xlink:label="ifrs-full_OtherCurrentReceivables_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="ifrs-full_OtherCurrentReceivables_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TradeAndOtherCurrentReceivables" xlink:label="ifrs-full_TradeAndOtherCurrentReceivables_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="ifrs-full_TradeAndOtherCurrentReceivables_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsDetails" xlink:type="extended" xlink:title="99941101 - Disclosure - Cash and Cash Equivalents (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalentsAbstract" xlink:label="CashAndCashEquivalentsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BalancesWithBanks" xlink:label="ifrs-full_BalancesWithBanks_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_BalancesWithBanks_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ShorttermDepositsClassifiedAsCashEquivalents" xlink:label="ifrs-full_ShorttermDepositsClassifiedAsCashEquivalents_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_ShorttermDepositsClassifiedAsCashEquivalents_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MoneyMarketFunds" xlink:label="prqr_MoneyMarketFunds_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="prqr_MoneyMarketFunds_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_CashAndCashEquivalents_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="7" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityShareCapitalDetails" xlink:type="extended" xlink:title="99941201 - Disclosure - Shareholders' Equity - Share capital (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalTable" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfShareCapitalAxis" xlink:label="ifrs-full_ClassesOfShareCapitalAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="ifrs-full_ClassesOfShareCapitalAxis_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfShareCapitalDomain" xlink:label="ifrs-full_ClassesOfShareCapitalDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalAxis_639089076753840967" xlink:to="ifrs-full_ClassesOfShareCapitalDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OrdinarySharesMember" xlink:label="ifrs-full_OrdinarySharesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalDomain_639089076753840967" xlink:to="ifrs-full_OrdinarySharesMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PreferenceSharesMember" xlink:label="ifrs-full_PreferenceSharesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalDomain_639089076753840967" xlink:to="ifrs-full_PreferenceSharesMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="ifrs-full_CounterpartiesAxis_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753840967" xlink:to="ifrs-full_CounterpartiesDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753840967" xlink:to="prqr_EliLillyAndCompanyMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RetrospectiveApplicationAndRetrospectiveRestatementAxis" xlink:label="ifrs-full_RetrospectiveApplicationAndRetrospectiveRestatementAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="ifrs-full_RetrospectiveApplicationAndRetrospectiveRestatementAxis_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RestatedMember" xlink:label="ifrs-full_RestatedMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RetrospectiveApplicationAndRetrospectiveRestatementAxis_639089076753840967" xlink:to="ifrs-full_RestatedMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PreviouslyStatedMember" xlink:label="ifrs-full_PreviouslyStatedMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RestatedMember_639089076753840967" xlink:to="ifrs-full_PreviouslyStatedMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalLineItems" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesIssued" xlink:label="ifrs-full_NumberOfSharesIssued_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_NumberOfSharesIssued_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfNewSharesIssuedForCash" xlink:label="prqr_NumberOfNewSharesIssuedForCash_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_NumberOfNewSharesIssuedForCash_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInNumberOfSharesThroughExerciseOfOptionsAndVestingOfRestrictedShareUnits" xlink:label="prqr_IncreaseDecreaseInNumberOfSharesThroughExerciseOfOptionsAndVestingOfRestrictedShareUnits_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseInNumberOfSharesThroughExerciseOfOptionsAndVestingOfRestrictedShareUnits_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInNumberOfSharesOutstandingThroughIssueTransferOfTreasuryShares" xlink:label="prqr_IncreaseDecreaseInNumberOfSharesOutstandingThroughIssueTransferOfTreasuryShares_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IncreaseDecreaseInNumberOfSharesOutstandingThroughIssueTransferOfTreasuryShares_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AuthorizedShareCapitalValue" xlink:label="prqr_AuthorizedShareCapitalValue_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_AuthorizedShareCapitalValue_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesIssued" xlink:label="ifrs-full_NumberOfSharesIssued_6390890767538409671" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_NumberOfSharesIssued_6390890767538409671" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesAuthorised" xlink:label="ifrs-full_NumberOfSharesAuthorised_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_NumberOfSharesAuthorised_639089076753840967" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ParValuePerShare" xlink:label="ifrs-full_ParValuePerShare_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_ParValuePerShare_639089076753840967" order="8" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesIssuedAndFullyPaid" xlink:label="ifrs-full_NumberOfSharesIssuedAndFullyPaid_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_NumberOfSharesIssuedAndFullyPaid_639089076753840967" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates" xlink:label="ifrs-full_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates_639089076753840967" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753840967" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GrossProceedsFromIssuingShares" xlink:label="prqr_GrossProceedsFromIssuingShares_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_GrossProceedsFromIssuingShares_639089076753840967" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ShareIssueRelatedCost" xlink:label="ifrs-full_ShareIssueRelatedCost_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_ShareIssueRelatedCost_639089076753840967" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IssueOfEquity" xlink:label="ifrs-full_IssueOfEquity_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_IssueOfEquity_639089076753840967" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquitySaleOfSharesDetails" xlink:type="extended" xlink:title="99941202 - Disclosure - Shareholders' Equity - Sale of shares (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract_1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalTable" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract_1" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsSaleOfStockAxis" xlink:label="prqr_IfrsSaleOfStockAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="prqr_IfrsSaleOfStockAxis_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsSaleOfStockDomain" xlink:label="prqr_IfrsSaleOfStockDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsSaleOfStockAxis_639089076753840967" xlink:to="prqr_IfrsSaleOfStockDomain_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ShelfRegistrationStatement2024Member" xlink:label="prqr_ShelfRegistrationStatement2024Member_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsSaleOfStockDomain_639089076753840967" xlink:to="prqr_ShelfRegistrationStatement2024Member_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember" xlink:label="prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639089076753840967" xlink:to="prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_October2024UnderwrittenPublicOfferingMember" xlink:label="prqr_October2024UnderwrittenPublicOfferingMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639089076753840967" xlink:to="prqr_October2024UnderwrittenPublicOfferingMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember" xlink:label="prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_October2024UnderwrittenPublicOfferingMember_639089076753840967" xlink:to="prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember" xlink:label="prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639089076753840967" xlink:to="prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalLineItems" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MaximumOfferingPriceInShelfRegistrationStatement" xlink:label="prqr_MaximumOfferingPriceInShelfRegistrationStatement_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_MaximumOfferingPriceInShelfRegistrationStatement_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement" xlink:label="prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsSaleOfStockPricePerShare" xlink:label="prqr_IfrsSaleOfStockPricePerShare_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IfrsSaleOfStockPricePerShare_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DurationOfUnderwritersOption" xlink:label="prqr_DurationOfUnderwritersOption_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_DurationOfUnderwritersOption_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfSharesCallableForOptionsIssued" xlink:label="prqr_NumberOfSharesCallableForOptionsIssued_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_NumberOfSharesCallableForOptionsIssued_639089076753840967" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromIssuingShares" xlink:label="ifrs-full_ProceedsFromIssuingShares_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_ProceedsFromIssuingShares_639089076753840967" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PaymentsForShareIssueCosts" xlink:label="ifrs-full_PaymentsForShareIssueCosts_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_PaymentsForShareIssueCosts_639089076753840967" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NetProceedsFromIssuingShares" xlink:label="prqr_NetProceedsFromIssuingShares_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_NetProceedsFromIssuingShares_639089076753840967" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PurchasePriceCapSharePurchaseAgreement" xlink:label="prqr_PurchasePriceCapSharePurchaseAgreement_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_PurchasePriceCapSharePurchaseAgreement_639089076753840967" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityShareOptionsDetails" xlink:type="extended" xlink:title="99941203 - Disclosure - Shareholders' Equity - Share options (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract_2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets" xlink:label="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract_2" xlink:to="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityShareOptionsAndRestrictedStockUnitsDetails" xlink:type="extended" xlink:title="99941204 - Disclosure - Shareholders' Equity - Share options and restricted stock units (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable" xlink:label="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfSharebasedPaymentArrangementsAxis" xlink:label="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfSharebasedPaymentArrangementsDomain" xlink:label="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" xlink:to="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_StockOptionsAndRestrictedStockUnitsRsusMember" xlink:label="prqr_StockOptionsAndRestrictedStockUnitsRsusMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753840967" xlink:to="prqr_StockOptionsAndRestrictedStockUnitsRsusMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ShareOptionsMember" xlink:label="ifrs-full_ShareOptionsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753840967" xlink:to="ifrs-full_ShareOptionsMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RestrictedShareUnitsMember" xlink:label="ifrs-full_RestrictedShareUnitsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753840967" xlink:to="ifrs-full_RestrictedShareUnitsMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639089076753840967" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsResearchAndDevelopmentExpenseMember" xlink:label="prqr_IfrsResearchAndDevelopmentExpenseMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" xlink:to="prqr_IfrsResearchAndDevelopmentExpenseMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsSellingGeneralAndAdministrativeExpensesMember" xlink:label="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639089076753840967" xlink:to="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2025/elts/srt-2025.xsd#srt_StatementScenarioAxis" xlink:label="srt_StatementScenarioAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="srt_StatementScenarioAxis_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2025/elts/srt-2025.xsd#srt_ScenarioUnspecifiedDomain" xlink:label="srt_ScenarioUnspecifiedDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_StatementScenarioAxis_639089076753840967" xlink:to="srt_ScenarioUnspecifiedDomain_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScenarioFourYearsVestingWith25PercentEveryYearMember" xlink:label="prqr_ScenarioFourYearsVestingWith25PercentEveryYearMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ScenarioUnspecifiedDomain_639089076753840967" xlink:to="prqr_ScenarioFourYearsVestingWith25PercentEveryYearMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScenarioFourYearsVestingInThirteenTranchesMember" xlink:label="prqr_ScenarioFourYearsVestingInThirteenTranchesMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ScenarioUnspecifiedDomain_639089076753840967" xlink:to="prqr_ScenarioFourYearsVestingInThirteenTranchesMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScenarioTwoYearsVestingWith25PercentEverySixMonthsMember" xlink:label="prqr_ScenarioTwoYearsVestingWith25PercentEverySixMonthsMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ScenarioUnspecifiedDomain_639089076753840967" xlink:to="prqr_ScenarioTwoYearsVestingWith25PercentEverySixMonthsMember_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalLineItems" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseFromSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets" xlink:label="ifrs-full_ExpenseFromSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_ExpenseFromSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod" xlink:label="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfTranches" xlink:label="prqr_NumberOfTranches_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_NumberOfTranches_639089076753840967" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate" xlink:label="prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate_639089076753840967" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AnnualVestingPercentage" xlink:label="prqr_AnnualVestingPercentage_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_AnnualVestingPercentage_639089076753840967" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_QuarterlyVestingPercentageAfterFirstTrancheIsVested" xlink:label="prqr_QuarterlyVestingPercentageAfterFirstTrancheIsVested_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_QuarterlyVestingPercentageAfterFirstTrancheIsVested_639089076753840967" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_BiannualVestingPercentage" xlink:label="prqr_BiannualVestingPercentage_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_BiannualVestingPercentage_639089076753840967" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod" xlink:label="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod_639089076753840967" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PeriodFollowingGrantDateThatOptionsAreAssumedToBeExercised" xlink:label="prqr_PeriodFollowingGrantDateThatOptionsAreAssumedToBeExercised_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="prqr_PeriodFollowingGrantDateThatOptionsAreAssumedToBeExercised_639089076753840967" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfRiskFreeInterestRateShareOptionsGranted" xlink:label="ifrs-full_DescriptionOfRiskFreeInterestRateShareOptionsGranted_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_DescriptionOfRiskFreeInterestRateShareOptionsGranted_639089076753840967" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfExpectedVolatilityShareOptionsGranted" xlink:label="ifrs-full_DescriptionOfExpectedVolatilityShareOptionsGranted_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_DescriptionOfExpectedVolatilityShareOptionsGranted_639089076753840967" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfOptionLifeShareOptionsGranted" xlink:label="ifrs-full_DescriptionOfOptionLifeShareOptionsGranted_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_DescriptionOfOptionLifeShareOptionsGranted_639089076753840967" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageFairValueAtMeasurementDateOtherEquityInstrumentsGranted" xlink:label="ifrs-full_WeightedAverageFairValueAtMeasurementDateOtherEquityInstrumentsGranted_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_WeightedAverageFairValueAtMeasurementDateOtherEquityInstrumentsGranted_639089076753840967" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted" xlink:label="ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639089076753840967" xlink:to="ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted_639089076753840967" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityMovementsInNumberOfOptionsOutstandingDetails" xlink:type="extended" xlink:title="99941205 - Disclosure - Shareholders' Equity - Movements in the number of options outstanding (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable" xlink:label="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_RangeAxis_639089076753840967" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076753840967" xlink:to="ifrs-full_RangeDomain_639089076753840967" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BottomOfRangeMember" xlink:label="ifrs-full_BottomOfRangeMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753840967" xlink:to="ifrs-full_BottomOfRangeMember_639089076753840967" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753840967" xlink:to="ifrs-full_TopOfRangeMember_639089076753840967" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfSharebasedPaymentArrangementsAxis" xlink:label="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfSharebasedPaymentArrangementsDomain" xlink:label="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsAxis_639089076753840967" xlink:to="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ShareOptionsMember" xlink:label="ifrs-full_ShareOptionsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfSharebasedPaymentArrangementsDomain_639089076753997245" xlink:to="ifrs-full_ShareOptionsMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ShareOptionsSubjectToNonMarketPerformanceConditionsMember" xlink:label="prqr_ShareOptionsSubjectToNonMarketPerformanceConditionsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ShareOptionsMember_639089076753997245" xlink:to="prqr_ShareOptionsSubjectToNonMarketPerformanceConditionsMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems" xlink:label="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639089076753840967" xlink:to="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageFairValueAtMeasurementDateShareOptionsGranted" xlink:label="ifrs-full_WeightedAverageFairValueAtMeasurementDateShareOptionsGranted_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageFairValueAtMeasurementDateShareOptionsGranted_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod" xlink:label="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="prqr_IfrsShareBasedCompensationArrangementByShareBasedPaymentAwardExpirationPeriod_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfOptionLifeShareOptionsGranted" xlink:label="ifrs-full_DescriptionOfOptionLifeShareOptionsGranted_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_DescriptionOfOptionLifeShareOptionsGranted_639089076753997245" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOutstandingShareOptions" xlink:label="ifrs-full_NumberOfOutstandingShareOptions_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfOutstandingShareOptions_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsForfeitedInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsForfeitedInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfShareOptionsForfeitedInSharebasedPaymentArrangement_639089076753997245" order="6" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsExercisedInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsExercisedInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfShareOptionsExercisedInSharebasedPaymentArrangement_639089076753997245" order="7" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsExpiredInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsExpiredInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfShareOptionsExpiredInSharebasedPaymentArrangement_639089076753997245" order="8" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOutstandingShareOptions" xlink:label="ifrs-full_NumberOfOutstandingShareOptions_6390890767539972451" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfOutstandingShareOptions_6390890767539972451" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsExercisableInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsExercisableInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfShareOptionsExercisableInSharebasedPaymentArrangement_639089076753997245" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019_639089076753997245" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsGrantedInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsGrantedInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsGrantedInSharebasedPaymentArrangement2019_639089076753997245" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsForfeitedInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsForfeitedInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsForfeitedInSharebasedPaymentArrangement2019_639089076753997245" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisedInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisedInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisedInSharebasedPaymentArrangement2019_639089076753997245" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsExpiredInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExpiredInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExpiredInSharebasedPaymentArrangement2019_639089076753997245" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019_6390890767539972451" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsOutstandingInSharebasedPaymentArrangement2019_6390890767539972451" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisableInSharebasedPaymentArrangement2019" xlink:label="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisableInSharebasedPaymentArrangement2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageExercisePriceOfShareOptionsExercisableInSharebasedPaymentArrangement2019_639089076753997245" order="17" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExercisePriceOfOutstandingShareOptions2019" xlink:label="ifrs-full_ExercisePriceOfOutstandingShareOptions2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_ExercisePriceOfOutstandingShareOptions2019_639089076753997245" order="18" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageSharePrice2019" xlink:label="ifrs-full_WeightedAverageSharePrice2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageSharePrice2019_639089076753997245" order="19" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019" xlink:label="ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639089076753997245" xlink:to="ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019_639089076753997245" order="20" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="6" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityMovementsInNumberOfRsusOutstandingDetails" xlink:type="extended" xlink:title="99941206 - Disclosure - Shareholders' Equity - Movements in the number of RSUs outstanding (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted" xlink:label="ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_NumberOfInstrumentsOtherEquityInstrumentsGranted_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOtherEquityInstrumentsForfeitedInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfOtherEquityInstrumentsForfeitedInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_NumberOfOtherEquityInstrumentsForfeitedInSharebasedPaymentArrangement_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOtherEquityInstrumentsExpiredInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfOtherEquityInstrumentsExpiredInSharebasedPaymentArrangement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_NumberOfOtherEquityInstrumentsExpiredInSharebasedPaymentArrangement_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement_6390890767539972451" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_NumberOfOtherEquityInstrumentsOutstandingInSharebasedPaymentArrangement_6390890767539972451" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowingsDetails" xlink:type="extended" xlink:title="99941301 - Disclosure - Borrowings (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsAbstract" xlink:label="BorrowingsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsByNameAxis" xlink:label="ifrs-full_BorrowingsByNameAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" xlink:to="ifrs-full_BorrowingsByNameAxis_639089076753997245" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsByNameDomain" xlink:label="ifrs-full_BorrowingsByNameDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameAxis_639089076753997245" xlink:to="ifrs-full_BorrowingsByNameDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_InnovationCreditMember" xlink:label="prqr_InnovationCreditMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameDomain_639089076753997245" xlink:to="prqr_InnovationCreditMember_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RvoInnovationCreditForCysticSepofarsenProgramMember" xlink:label="prqr_RvoInnovationCreditForCysticSepofarsenProgramMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_InnovationCreditMember_639089076753997245" xlink:to="prqr_RvoInnovationCreditForCysticSepofarsenProgramMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsConvertibleDebtMember" xlink:label="prqr_IfrsConvertibleDebtMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameDomain_639089076753997245" xlink:to="prqr_IfrsConvertibleDebtMember_639089076753997245" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConvertibleLoansAmylonTherapeuticsB.v.Member" xlink:label="prqr_ConvertibleLoansAmylonTherapeuticsB.v.Member_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsConvertibleDebtMember_639089076753997245" xlink:to="prqr_ConvertibleLoansAmylonTherapeuticsB.v.Member_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingMember" xlink:label="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsConvertibleDebtMember_639089076753997245" xlink:to="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConvertibleDebtPontifaxMedisonDebtFinancingMember" xlink:label="prqr_ConvertibleDebtPontifaxMedisonDebtFinancingMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingMember_639089076753997245" xlink:to="prqr_ConvertibleDebtPontifaxMedisonDebtFinancingMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConvertibleDebtKreosCapitalDebtFinancingMember" xlink:label="prqr_ConvertibleDebtKreosCapitalDebtFinancingMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingMember_639089076753997245" xlink:to="prqr_ConvertibleDebtKreosCapitalDebtFinancingMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingAmendedAgreementMember" xlink:label="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingAmendedAgreementMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameDomain_639089076753997245" xlink:to="prqr_ConvertibleDebtPontifaxMedisonAndKreosCapitalDebtFinancingAmendedAgreementMember_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" xlink:to="ifrs-full_RangeAxis_639089076753997245" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076753997245" xlink:to="ifrs-full_RangeDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753997245" xlink:to="ifrs-full_TopOfRangeMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_Borrowings" xlink:label="ifrs-full_Borrowings_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_Borrowings_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="7" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestPayable" xlink:label="ifrs-full_InterestPayable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_InterestPayable_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings" xlink:label="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NotionalAmount" xlink:label="ifrs-full_NotionalAmount_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_NotionalAmount_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RepaymentsOfBorrowingsClassifiedAsFinancingActivities" xlink:label="ifrs-full_RepaymentsOfBorrowingsClassifiedAsFinancingActivities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_RepaymentsOfBorrowingsClassifiedAsFinancingActivities_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ConditionalWaiverOfDebtIncludingAccruedInterest" xlink:label="prqr_ConditionalWaiverOfDebtIncludingAccruedInterest_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_ConditionalWaiverOfDebtIncludingAccruedInterest_639089076753997245" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid" xlink:label="ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_GainLossArisingFromDifferenceBetweenCarryingAmountOfFinancialLiabilityExtinguishedAndConsiderationPaid_639089076753997245" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsInterestRate" xlink:label="ifrs-full_BorrowingsInterestRate_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_BorrowingsInterestRate_639089076753997245" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities" xlink:label="ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_ProceedsFromBorrowingsClassifiedAsFinancingActivities_639089076753997245" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfTranches" xlink:label="prqr_NumberOfTranches_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_NumberOfTranches_639089076753997245" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsLineOfCreditFacilityMaximumBorrowingCapacityPerTranche" xlink:label="prqr_IfrsLineOfCreditFacilityMaximumBorrowingCapacityPerTranche_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IfrsLineOfCreditFacilityMaximumBorrowingCapacityPerTranche_639089076753997245" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsDebtInstrumentTerm" xlink:label="prqr_IfrsDebtInstrumentTerm_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IfrsDebtInstrumentTerm_639089076753997245" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsDebtInstrumentInterestOnlyPaymentTerm" xlink:label="prqr_IfrsDebtInstrumentInterestOnlyPaymentTerm_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IfrsDebtInstrumentInterestOnlyPaymentTerm_639089076753997245" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfTranchesFromOriginalAgreementReplacedWithAmendmentAgreement" xlink:label="prqr_NumberOfTranchesFromOriginalAgreementReplacedWithAmendmentAgreement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_NumberOfTranchesFromOriginalAgreementReplacedWithAmendmentAgreement_639089076753997245" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfSharesExercisableForIssuedWarrants" xlink:label="prqr_NumberOfSharesExercisableForIssuedWarrants_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_NumberOfSharesExercisableForIssuedWarrants_639089076753997245" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WarrantsEconomicLifetime" xlink:label="prqr_WarrantsEconomicLifetime_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_WarrantsEconomicLifetime_639089076753997245" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076753997245" order="17" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076753997245" order="18" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowingsReconciliationOfMovementsOfLiabilitiesToCashFlowsArisingFromFinancingActivitiesDetails" xlink:type="extended" xlink:title="99941302 - Disclosure - Borrowings - Reconciliation of movements of liabilities to cash flows arising from financing activities (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsAbstract" xlink:label="ifrs-full_BorrowingsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LiabilitiesArisingFromFinancingActivitiesAxis" xlink:label="ifrs-full_LiabilitiesArisingFromFinancingActivitiesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" xlink:to="ifrs-full_LiabilitiesArisingFromFinancingActivitiesAxis_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LiabilitiesArisingFromFinancingActivitiesDomain" xlink:label="ifrs-full_LiabilitiesArisingFromFinancingActivitiesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesArisingFromFinancingActivitiesAxis_639089076753997245" xlink:to="ifrs-full_LiabilitiesArisingFromFinancingActivitiesDomain_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LongtermBorrowingsMember" xlink:label="ifrs-full_LongtermBorrowingsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesArisingFromFinancingActivitiesDomain_639089076753997245" xlink:to="ifrs-full_LongtermBorrowingsMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LeaseLiabilitiesMember" xlink:label="ifrs-full_LeaseLiabilitiesMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesArisingFromFinancingActivitiesDomain_639089076753997245" xlink:to="ifrs-full_LeaseLiabilitiesMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems" xlink:label="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LiabilitiesArisingFromFinancingActivities" xlink:label="ifrs-full_LiabilitiesArisingFromFinancingActivities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_LiabilitiesArisingFromFinancingActivities_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DecreaseInLiabilitiesArisingFromFinancingActivitiesThroughRepayments" xlink:label="prqr_DecreaseInLiabilitiesArisingFromFinancingActivitiesThroughRepayments_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_DecreaseInLiabilitiesArisingFromFinancingActivitiesThroughRepayments_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseInLiabilitiesArisingFromFinancingActivitiesThroughInterestExpense" xlink:label="prqr_IncreaseInLiabilitiesArisingFromFinancingActivitiesThroughInterestExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IncreaseInLiabilitiesArisingFromFinancingActivitiesThroughInterestExpense_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInLiabilitiesArisingFromFinancingActivitiesThroughLeaseAmendments" xlink:label="prqr_IncreaseDecreaseInLiabilitiesArisingFromFinancingActivitiesThroughLeaseAmendments_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="prqr_IncreaseDecreaseInLiabilitiesArisingFromFinancingActivitiesThroughLeaseAmendments_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LiabilitiesArisingFromFinancingActivities" xlink:label="ifrs-full_LiabilitiesArisingFromFinancingActivities_6390890767539972451" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639089076753997245" xlink:to="ifrs-full_LiabilitiesArisingFromFinancingActivities_6390890767539972451" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncomeSummaryOfDeferredIncomeDetails" xlink:type="extended" xlink:title="99941401 - Disclosure - Deferred Income - Summary of deferred income (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract_2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_2" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_CounterpartiesAxis_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753997245" xlink:to="ifrs-full_CounterpartiesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753997245" xlink:to="prqr_EliLillyAndCompanyMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RettSyndromeResearchTrustMember" xlink:label="prqr_RettSyndromeResearchTrustMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753997245" xlink:to="prqr_RettSyndromeResearchTrustMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities" xlink:label="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities" xlink:label="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncomeSummaryOfDeferredIncomeUndiscountedDeferredIncomeByMaturityDetails" xlink:type="extended" xlink:title="99941402 - Disclosure - Deferred Income - Summary of deferred income - Undiscounted deferred income by maturity (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract_3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateTable" xlink:label="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_3" xlink:to="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateTable_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityAxis" xlink:label="ifrs-full_MaturityAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateTable_639089076753997245" xlink:to="ifrs-full_MaturityAxis_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityDomain" xlink:label="ifrs-full_MaturityDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityAxis_639089076753997245" xlink:to="ifrs-full_MaturityDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NotLaterThanOneYearMember" xlink:label="ifrs-full_NotLaterThanOneYearMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753997245" xlink:to="ifrs-full_NotLaterThanOneYearMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember" xlink:label="ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753997245" xlink:to="ifrs-full_LaterThanOneYearAndNotLaterThanTwoYearsMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember" xlink:label="ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076753997245" xlink:to="ifrs-full_LaterThanTwoYearsAndNotLaterThanFiveYearsMember_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateLineItems" xlink:label="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateLineItems_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DeferredIncomeUndiscounted" xlink:label="prqr_DeferredIncomeUndiscounted_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfAmountsToBeRecoveredOrSettledAfterTwelveMonthsForClassesOfAssetsAndLiabilitiesThatContainAmountsToBeRecoveredOrSettledBothNoMoreAndMoreThanTwelveMonthsAfterReportingDateLineItems_639089076753997245" xlink:to="prqr_DeferredIncomeUndiscounted_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherCurrentLiabiltiesDetails" xlink:type="extended" xlink:title="99941501 - Disclosure - Other Current Liabilties (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OtherCurrentLiabilitiesAbstract" xlink:label="prqr_OtherCurrentLiabilitiesAbstract_1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherCurrentLiabilities" xlink:label="ifrs-full_OtherCurrentLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherCurrentLiabilitiesAbstract_1" xlink:to="ifrs-full_OtherCurrentLiabilities_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenueSummaryOfRevenueRecognizedDetails" xlink:type="extended" xlink:title="99941601 - Disclosure - Revenue - Summary of revenue recognized (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueAbstract" xlink:label="ifrs-full_RevenueAbstract_1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RevenueFromContractsWithCustomersUpfrontConsideration" xlink:label="prqr_RevenueFromContractsWithCustomersUpfrontConsideration_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract_1" xlink:to="prqr_RevenueFromContractsWithCustomersUpfrontConsideration_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RevenueFromContractsWithCustomersMilestonesAchieved" xlink:label="prqr_RevenueFromContractsWithCustomersMilestonesAchieved_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract_1" xlink:to="prqr_RevenueFromContractsWithCustomersMilestonesAchieved_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueFromContractsWithCustomers" xlink:label="ifrs-full_RevenueFromContractsWithCustomers_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract_1" xlink:to="ifrs-full_RevenueFromContractsWithCustomers_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenueSummaryOfChangesInCurrentAndNonCurrentDeferredRevenueDetails" xlink:type="extended" xlink:title="99941602 - Disclosure - Revenue - Summary of changes in current and non-current deferred revenue (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueAbstract" xlink:label="ifrs-full_RevenueAbstract_2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract_2" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_CounterpartiesAxis_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753997245" xlink:to="ifrs-full_CounterpartiesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753997245" xlink:to="prqr_EliLillyAndCompanyMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProductsAndServicesAxis" xlink:label="ifrs-full_ProductsAndServicesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_ProductsAndServicesAxis_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProductsAndServicesDomain" xlink:label="ifrs-full_ProductsAndServicesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesAxis_639089076753997245" xlink:to="ifrs-full_ProductsAndServicesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EquityConsiderationMember" xlink:label="prqr_EquityConsiderationMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesDomain_639089076753997245" xlink:to="prqr_EquityConsiderationMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseInDeferredIncomeThroughMilestonesAchieved" xlink:label="prqr_IncreaseInDeferredIncomeThroughMilestonesAchieved_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_IncreaseInDeferredIncomeThroughMilestonesAchieved_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DecreaseInDeferredIncomeThroughRevenueRecognised" xlink:label="prqr_DecreaseInDeferredIncomeThroughRevenueRecognised_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_DecreaseInDeferredIncomeThroughRevenueRecognised_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedTerseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_6390890767539972451" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_6390890767539972451" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_FundingReceivedUnderAgreement" xlink:label="prqr_FundingReceivedUnderAgreement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_FundingReceivedUnderAgreement_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenueAdditionalInformationDetails" xlink:type="extended" xlink:title="99941603 - Disclosure - Revenue - Additional information (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RevenueAbstract" xlink:label="RevenueAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="RevenueAbstract" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesAxis" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753997245" order="1" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SignificantInvestmentsInAssociatesDomain" xlink:label="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesAxis_639089076753997245" xlink:to="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_YarrowBiotechnologyMember" xlink:label="prqr_YarrowBiotechnologyMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInAssociatesDomain_639089076753997245" xlink:to="prqr_YarrowBiotechnologyMember_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_CounterpartiesAxis_639089076753997245" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753997245" xlink:to="ifrs-full_CounterpartiesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753997245" xlink:to="prqr_EliLillyAndCompanyMember_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProductsAndServicesAxis" xlink:label="ifrs-full_ProductsAndServicesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_ProductsAndServicesAxis_639089076753997245" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProductsAndServicesDomain" xlink:label="ifrs-full_ProductsAndServicesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesAxis_639089076753997245" xlink:to="ifrs-full_ProductsAndServicesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_EquityConsiderationMember" xlink:label="prqr_EquityConsiderationMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesDomain_639089076753997245" xlink:to="prqr_EquityConsiderationMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MilestonePaymentsMember" xlink:label="prqr_MilestonePaymentsMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesDomain_639089076753997245" xlink:to="prqr_MilestonePaymentsMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639089076753997245" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" order="4" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProportionOfOwnershipInterestInAssociate" xlink:label="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076753997245" order="2" use="optional" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesIssued" xlink:label="ifrs-full_NumberOfSharesIssued_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_NumberOfSharesIssued_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromIssuingShares" xlink:label="ifrs-full_ProceedsFromIssuingShares_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_ProceedsFromIssuingShares_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GrossProceedsFromIssuingShares" xlink:label="prqr_GrossProceedsFromIssuingShares_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_GrossProceedsFromIssuingShares_639089076753997245" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DiscountOnIssueOfShares" xlink:label="prqr_DiscountOnIssueOfShares_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_DiscountOnIssueOfShares_639089076753997245" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CollaborationAgreementUpfrontPaymentReceived" xlink:label="prqr_CollaborationAgreementUpfrontPaymentReceived_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_CollaborationAgreementUpfrontPaymentReceived_639089076753997245" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership" xlink:label="prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership_639089076753997245" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfPerformanceObligationsInCollaborationAgreement" xlink:label="prqr_NumberOfPerformanceObligationsInCollaborationAgreement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="prqr_NumberOfPerformanceObligationsInCollaborationAgreement_639089076753997245" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices" xlink:label="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639089076753997245" xlink:to="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639089076753997245" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherIncomeDetails" xlink:type="extended" xlink:title="99941701 - Disclosure - Other Income (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GainsLossesOnSaleOfIntellectualProperty" xlink:label="prqr_GainsLossesOnSaleOfIntellectualProperty_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_GainsLossesOnSaleOfIntellectualProperty_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsRevenueFromGrants" xlink:label="prqr_IfrsRevenueFromGrants_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_IfrsRevenueFromGrants_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MiscellaneousOtherOperatingIncome" xlink:label="ifrs-full_MiscellaneousOtherOperatingIncome_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="ifrs-full_MiscellaneousOtherOperatingIncome_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OtherIncome" xlink:label="ifrs-full_OtherIncome_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="ifrs-full_OtherIncome_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherIncomeNarrativeDetails" xlink:type="extended" xlink:title="99941702 - Disclosure - Other Income - Narrative (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OtherIncomeTable" xlink:label="prqr_OtherIncomeTable_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_OtherIncomeTable_639089076753997245" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfContractsAxis" xlink:label="ifrs-full_TypesOfContractsAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639089076753997245" xlink:to="ifrs-full_TypesOfContractsAxis_639089076753997245" order="1" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TypesOfContractsDomain" xlink:label="ifrs-full_TypesOfContractsDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfContractsAxis_639089076753997245" xlink:to="ifrs-full_TypesOfContractsDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ClinicalSupportAgreementMember" xlink:label="prqr_ClinicalSupportAgreementMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfContractsDomain_639089076753997245" xlink:to="prqr_ClinicalSupportAgreementMember_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseOneMember" xlink:label="prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseOneMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfContractsDomain_639089076753997245" xlink:to="prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseOneMember_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseTwoMember" xlink:label="prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseTwoMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TypesOfContractsDomain_639089076753997245" xlink:to="prqr_AgreementWithRsrtThatFocusesOnDesignAndDevelopmentOfEditingOligonucleotidesPhaseTwoMember_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesAxis" xlink:label="ifrs-full_CounterpartiesAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639089076753997245" xlink:to="ifrs-full_CounterpartiesAxis_639089076753997245" order="2" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639089076753997245" xlink:to="ifrs-full_CounterpartiesDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_FoundationFightingBlindnessMember" xlink:label="prqr_FoundationFightingBlindnessMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639089076753997245" xlink:to="prqr_FoundationFightingBlindnessMember_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis" xlink:label="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639089076753997245" xlink:to="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain" xlink:label="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076753997245" xlink:to="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076753997245" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SepofarsenAndUltevursenMember" xlink:label="prqr_SepofarsenAndUltevursenMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076753997245" xlink:to="prqr_SepofarsenAndUltevursenMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639089076753997245" xlink:to="ifrs-full_RangeAxis_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076753997245" xlink:to="ifrs-full_RangeDomain_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076753997245" xlink:to="ifrs-full_TopOfRangeMember_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OtherIncomeLineItems" xlink:label="prqr_OtherIncomeLineItems_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639089076753997245" xlink:to="prqr_OtherIncomeLineItems_639089076753997245" order="5" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MiscellaneousOtherOperatingIncome" xlink:label="ifrs-full_MiscellaneousOtherOperatingIncome_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="ifrs-full_MiscellaneousOtherOperatingIncome_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_FundingReceivableUnderAgreement" xlink:label="prqr_FundingReceivableUnderAgreement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_FundingReceivableUnderAgreement_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsRevenueFromGrants" xlink:label="prqr_IfrsRevenueFromGrants_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_IfrsRevenueFromGrants_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GrossProceedsFromSaleOfIntellectualProperty" xlink:label="prqr_GrossProceedsFromSaleOfIntellectualProperty_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_GrossProceedsFromSaleOfIntellectualProperty_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualProperty" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualProperty_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualProperty_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GainsLossesOnSaleOfIntellectualProperty" xlink:label="prqr_GainsLossesOnSaleOfIntellectualProperty_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_GainsLossesOnSaleOfIntellectualProperty_639089076753997245" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualPropertyRepaymentOfGrants" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualPropertyRepaymentOfGrants_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualPropertyRepaymentOfGrants_639089076753997245" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualPropertyFinancialAdvisoryFees" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualPropertyFinancialAdvisoryFees_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualPropertyFinancialAdvisoryFees_639089076753997245" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualPropertyIncentivePayments" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualPropertyIncentivePayments_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualPropertyIncentivePayments_639089076753997245" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualPropertyAssignmentAndSuccessFees" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualPropertyAssignmentAndSuccessFees_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualPropertyAssignmentAndSuccessFees_639089076753997245" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TransactionCostsOnSaleOfIntellectualPropertyOtherCosts" xlink:label="prqr_TransactionCostsOnSaleOfIntellectualPropertyOtherCosts_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_TransactionCostsOnSaleOfIntellectualPropertyOtherCosts_639089076753997245" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities" xlink:label="ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="ifrs-full_ProceedsFromSalesOfIntangibleAssetsClassifiedAsInvestingActivities_639089076753997245" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MaximumGrantReceivableForInitialPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639089076753997245" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MaximumGrantReceivableForAdditionalPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639089076753997245" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076753997245" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076753997245" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WarrantsEconomicLifetime" xlink:label="prqr_WarrantsEconomicLifetime_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_WarrantsEconomicLifetime_639089076753997245" order="17" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices" xlink:label="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639089076753997245" order="18" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_FundingReceivedUnderAgreement" xlink:label="prqr_FundingReceivedUnderAgreement_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639089076753997245" xlink:to="prqr_FundingReceivedUnderAgreement_639089076753997245" order="19" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOperatingCostsDetails" xlink:type="extended" xlink:title="99941801 - Disclosure - Operating Costs (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseByNatureAbstract" xlink:label="ifrs-full_ExpenseByNatureAbstract_3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EmployeeBenefitsExpense" xlink:label="ifrs-full_EmployeeBenefitsExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="ifrs-full_EmployeeBenefitsExpense_639089076753997245" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ExternalResearchAndDevelopmentExpenses" xlink:label="prqr_ExternalResearchAndDevelopmentExpenses_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="prqr_ExternalResearchAndDevelopmentExpenses_639089076753997245" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LaboratoryAndOtherConsumablesExpenses" xlink:label="prqr_LaboratoryAndOtherConsumablesExpenses_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="prqr_LaboratoryAndOtherConsumablesExpenses_639089076753997245" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AdvisoryAndLegalExpenses" xlink:label="prqr_AdvisoryAndLegalExpenses_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="prqr_AdvisoryAndLegalExpenses_639089076753997245" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InsuranceExpense" xlink:label="ifrs-full_InsuranceExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="ifrs-full_InsuranceExpense_639089076753997245" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DepreciationExpense" xlink:label="ifrs-full_DepreciationExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="ifrs-full_DepreciationExpense_639089076753997245" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PatentAndLicenseExpense" xlink:label="prqr_PatentAndLicenseExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="prqr_PatentAndLicenseExpense_639089076753997245" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MiscellaneousOtherOperatingExpense" xlink:label="ifrs-full_MiscellaneousOtherOperatingExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="ifrs-full_MiscellaneousOtherOperatingExpense_639089076753997245" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_OperatingExpense" xlink:label="ifrs-full_OperatingExpense_639089076753997245" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ExpenseByNatureAbstract_3" xlink:to="ifrs-full_OperatingExpense_639089076753997245" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEmployeeBenefitsDetails" xlink:type="extended" xlink:title="99941901 - Disclosure - Employee Benefits (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfDefinedBenefitPlansAbstract" xlink:label="DisclosureOfDefinedBenefitPlansAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfGeographicalAreasTable" xlink:label="ifrs-full_DisclosureOfGeographicalAreasTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfDefinedBenefitPlansAbstract" xlink:to="ifrs-full_DisclosureOfGeographicalAreasTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GeographicalAreasAxis" xlink:label="ifrs-full_GeographicalAreasAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasTable_639089076754154299" xlink:to="ifrs-full_GeographicalAreasAxis_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GeographicalAreasDomain" xlink:label="ifrs-full_GeographicalAreasDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasAxis_639089076754154299" xlink:to="ifrs-full_GeographicalAreasDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/country/2025/country-2025.xsd#country_NL" xlink:label="country_NL_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasDomain_639089076754154299" xlink:to="country_NL_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfGeographicalAreasLineItems" xlink:label="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WagesAndSalaries" xlink:label="ifrs-full_WagesAndSalaries_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_WagesAndSalaries_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_SocialSecurityContributions" xlink:label="ifrs-full_SocialSecurityContributions_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_SocialSecurityContributions_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PostemploymentBenefitExpenseDefinedContributionPlans" xlink:label="ifrs-full_PostemploymentBenefitExpenseDefinedContributionPlans_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_PostemploymentBenefitExpenseDefinedContributionPlans_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets" xlink:label="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EmployeeBenefitsExpense" xlink:label="ifrs-full_EmployeeBenefitsExpense_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_EmployeeBenefitsExpense_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AverageNumberOfEmployees" xlink:label="ifrs-full_AverageNumberOfEmployees_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_AverageNumberOfEmployees_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfFullTimeEmployeesResearchAndDevelopment" xlink:label="prqr_NumberOfFullTimeEmployeesResearchAndDevelopment_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="prqr_NumberOfFullTimeEmployeesResearchAndDevelopment_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfFullTimeEmployeesGeneralAndAdministrative" xlink:label="prqr_NumberOfFullTimeEmployeesGeneralAndAdministrative_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="prqr_NumberOfFullTimeEmployeesGeneralAndAdministrative_639089076754154299" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfEmployees" xlink:label="ifrs-full_NumberOfEmployees_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="ifrs-full_NumberOfEmployees_639089076754154299" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WagesAndSalariesResearchAndDevelopmentTaxCreditSubsidy" xlink:label="prqr_WagesAndSalariesResearchAndDevelopmentTaxCreditSubsidy_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfGeographicalAreasLineItems_639089076754154299" xlink:to="prqr_WagesAndSalariesResearchAndDevelopmentTaxCreditSubsidy_639089076754154299" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureFinancialIncomeAndExpenseDetails" xlink:type="extended" xlink:title="99942001 - Disclosure - Financial Income and Expense (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:label="DisclosureOfFinancialIncomeAndExpenseAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestIncomeOnCashAndCashEquivalents" xlink:label="ifrs-full_InterestIncomeOnCashAndCashEquivalents_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_InterestIncomeOnCashAndCashEquivalents_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_InterestCostsOnCurrentAccountsAndDeposits" xlink:label="prqr_InterestCostsOnCurrentAccountsAndDeposits_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="prqr_InterestCostsOnCurrentAccountsAndDeposits_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestExpenseOnLeaseLiabilities" xlink:label="ifrs-full_InterestExpenseOnLeaseLiabilities_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_InterestExpenseOnLeaseLiabilities_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestExpenseOnBorrowings" xlink:label="ifrs-full_InterestExpenseOnBorrowings_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_InterestExpenseOnBorrowings_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainsLossesOnExchangeDifferencesOnTranslationRecognisedInProfitOrLoss" xlink:label="ifrs-full_GainsLossesOnExchangeDifferencesOnTranslationRecognisedInProfitOrLoss_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_GainsLossesOnExchangeDifferencesOnTranslationRecognisedInProfitOrLoss_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinanceIncomeCost" xlink:label="ifrs-full_FinanceIncomeCost_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_FinanceIncomeCost_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinanceIncome" xlink:label="ifrs-full_FinanceIncome_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_FinanceIncome_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinanceCosts" xlink:label="ifrs-full_FinanceCosts_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_FinanceCosts_639089076754154299" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestExpense" xlink:label="ifrs-full_InterestExpense_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_InterestExpense_639089076754154299" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NetForeignExchangeLoss" xlink:label="ifrs-full_NetForeignExchangeLoss_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfFinancialIncomeAndExpenseAbstract" xlink:to="ifrs-full_NetForeignExchangeLoss_639089076754154299" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureResultsRelatedToFinancialLiabilitiesMeasuredAtFairValueThroughProfitOrLossDetails" xlink:type="extended" xlink:title="99942101 - Disclosure - Results related to financial liabilities measured at fair value through profit or loss (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" xlink:label="ifrs-full_FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinancialLiabilitiesTable" xlink:label="ifrs-full_DisclosureOfFinancialLiabilitiesTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_FinancialLiabilitiesAtFairValueThroughProfitOrLossAbstract" xlink:to="ifrs-full_DisclosureOfFinancialLiabilitiesTable_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialLiabilitiesAxis" xlink:label="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfFinancialLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfFinancialLiabilitiesDomain" xlink:label="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesAxis_639089076754154299" xlink:to="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WarrantsToRettSyndromeResearchTrustMember" xlink:label="prqr_WarrantsToRettSyndromeResearchTrustMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076754154299" xlink:to="prqr_WarrantsToRettSyndromeResearchTrustMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WarrantsFromConvertibleLoansMember" xlink:label="prqr_WarrantsFromConvertibleLoansMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfFinancialLiabilitiesDomain_639089076754154299" xlink:to="prqr_WarrantsFromConvertibleLoansMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfFinancialLiabilitiesLineItems" xlink:label="ifrs-full_DisclosureOfFinancialLiabilitiesLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfFinancialLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfFinancialLiabilitiesLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss" xlink:label="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfFinancialLiabilitiesLineItems_639089076754154299" xlink:to="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxesDetails" xlink:type="extended" xlink:title="99942201 - Disclosure - Income Taxes (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" xlink:label="MajorComponentsOfTaxExpenseIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="MajorComponentsOfTaxExpenseIncomeAbstract" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_UnusedNonDeductibleInterestExpensesMember" xlink:label="prqr_UnusedNonDeductibleInterestExpensesMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" xlink:to="prqr_UnusedNonDeductibleInterestExpensesMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AccountingProfit" xlink:label="ifrs-full_AccountingProfit_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_AccountingProfit_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TaxExpenseIncomeAtApplicableTaxRate" xlink:label="ifrs-full_TaxExpenseIncomeAtApplicableTaxRate_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_TaxExpenseIncomeAtApplicableTaxRate_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TaxEffectOfForeignTaxRates" xlink:label="ifrs-full_TaxEffectOfForeignTaxRates_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_TaxEffectOfForeignTaxRates_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TaxEffectOfNonTaxableGainsNonDeductibleExpensesInDeterminingTaxableProfitTaxLoss" xlink:label="prqr_TaxEffectOfNonTaxableGainsNonDeductibleExpensesInDeterminingTaxableProfitTaxLoss_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="prqr_TaxEffectOfNonTaxableGainsNonDeductibleExpensesInDeterminingTaxableProfitTaxLoss_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TaxEffectOfShareAndLoanIssueExpendituresThatAreTaxable" xlink:label="prqr_TaxEffectOfShareAndLoanIssueExpendituresThatAreTaxable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="prqr_TaxEffectOfShareAndLoanIssueExpendituresThatAreTaxable_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TaxEffectOfUnrecognizedDeductibleTemporaryDifferences" xlink:label="prqr_TaxEffectOfUnrecognizedDeductibleTemporaryDifferences_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="prqr_TaxEffectOfUnrecognizedDeductibleTemporaryDifferences_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TaxEffectOfTaxLosses" xlink:label="ifrs-full_TaxEffectOfTaxLosses_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_TaxEffectOfTaxLosses_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="6" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TaxEffectOfTrueUpForPriorYear" xlink:label="prqr_TaxEffectOfTrueUpForPriorYear_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="prqr_TaxEffectOfTrueUpForPriorYear_639089076754154299" order="8" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IncomeTaxExpenseContinuingOperations" xlink:label="ifrs-full_IncomeTaxExpenseContinuingOperations_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_IncomeTaxExpenseContinuingOperations_639089076754154299" order="9" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedTotalLabel" priority="9" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AverageEffectiveTaxRate" xlink:label="ifrs-full_AverageEffectiveTaxRate_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_AverageEffectiveTaxRate_639089076754154299" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ApplicableTaxRate" xlink:label="ifrs-full_ApplicableTaxRate_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_ApplicableTaxRate_639089076754154299" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeductibleTemporaryDifferencesForWhichNoDeferredTaxAssetIsRecognised" xlink:label="ifrs-full_DeductibleTemporaryDifferencesForWhichNoDeferredTaxAssetIsRecognised_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_DeductibleTemporaryDifferencesForWhichNoDeferredTaxAssetIsRecognised_639089076754154299" order="12" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_UnusedTaxLossesForWhichNoDeferredTaxAssetRecognised" xlink:label="ifrs-full_UnusedTaxLossesForWhichNoDeferredTaxAssetRecognised_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_UnusedTaxLossesForWhichNoDeferredTaxAssetRecognised_639089076754154299" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxesDeferredTaxDetails" xlink:type="extended" xlink:title="99942202 - Disclosure - Income taxes - Deferred tax (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" xlink:label="ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain" xlink:label="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsAxis_639089076754154299" xlink:to="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_TemporaryDifferencesOnRightOfUseAssetsAndRelatedLeaseLiabilitiesMember" xlink:label="prqr_TemporaryDifferencesOnRightOfUseAssetsAndRelatedLeaseLiabilitiesMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsDomain_639089076754154299" xlink:to="prqr_TemporaryDifferencesOnRightOfUseAssetsAndRelatedLeaseLiabilitiesMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems" xlink:label="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredTaxLiabilities" xlink:label="ifrs-full_DeferredTaxLiabilities_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_DeferredTaxLiabilities_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DeferredTaxAssets" xlink:label="ifrs-full_DeferredTaxAssets_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTemporaryDifferenceUnusedTaxLossesAndUnusedTaxCreditsLineItems_639089076754154299" xlink:to="ifrs-full_DeferredTaxAssets_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEarningsPerShareDetails" xlink:type="extended" xlink:title="99942301 - Disclosure - Earnings Per Share (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_EarningsPerShareAbstract" xlink:label="EarningsPerShareAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProfitLossAttributableToOrdinaryEquityHoldersOfParentEntity" xlink:label="ifrs-full_ProfitLossAttributableToOrdinaryEquityHoldersOfParentEntity_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_ProfitLossAttributableToOrdinaryEquityHoldersOfParentEntity_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageShares" xlink:label="ifrs-full_WeightedAverageShares_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_WeightedAverageShares_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdjustedWeightedAverageShares" xlink:label="ifrs-full_AdjustedWeightedAverageShares_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_AdjustedWeightedAverageShares_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BasicEarningsLossPerShare" xlink:label="ifrs-full_BasicEarningsLossPerShare_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_BasicEarningsLossPerShare_639089076754154299" order="4" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DilutedEarningsLossPerShare" xlink:label="ifrs-full_DilutedEarningsLossPerShare_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="EarningsPerShareAbstract" xlink:to="ifrs-full_DilutedEarningsLossPerShare_639089076754154299" order="5" use="optional" priority="2" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureLeasesDetails" xlink:type="extended" xlink:title="99942401 - Disclosure - Leases (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_PresentationOfLeasesForLesseeAbstract" xlink:label="PresentationOfLeasesForLesseeAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable" xlink:label="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="PresentationOfLeasesForLesseeAbstract" xlink:to="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639089076754154299" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain" xlink:label="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639089076754154299" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OfficeAndLaboratoryFacilityMember" xlink:label="prqr_OfficeAndLaboratoryFacilityMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639089076754154299" xlink:to="prqr_OfficeAndLaboratoryFacilityMember_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GeographicalAreasAxis" xlink:label="ifrs-full_GeographicalAreasAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639089076754154299" xlink:to="ifrs-full_GeographicalAreasAxis_639089076754154299" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GeographicalAreasDomain" xlink:label="ifrs-full_GeographicalAreasDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasAxis_639089076754154299" xlink:to="ifrs-full_GeographicalAreasDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LeidenNetherlandsMember" xlink:label="prqr_LeidenNetherlandsMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasDomain_639089076754154299" xlink:to="prqr_LeidenNetherlandsMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems" xlink:label="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AreaOfPropertyUnderLease" xlink:label="prqr_AreaOfPropertyUnderLease_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_AreaOfPropertyUnderLease_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsLesseeOperatingLeaseRenewalTerm" xlink:label="prqr_IfrsLesseeOperatingLeaseRenewalTerm_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_IfrsLesseeOperatingLeaseRenewalTerm_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_LeaseLiabilities" xlink:label="ifrs-full_LeaseLiabilities_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_LeaseLiabilities_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RightofuseAssets" xlink:label="ifrs-full_RightofuseAssets_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_RightofuseAssets_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DepreciationRightofuseAssets" xlink:label="ifrs-full_DepreciationRightofuseAssets_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_DepreciationRightofuseAssets_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_InterestExpenseOnLeaseLiabilities" xlink:label="ifrs-full_InterestExpenseOnLeaseLiabilities_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_InterestExpenseOnLeaseLiabilities_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExpenseRelatingToShorttermLeasesForWhichRecognitionExemptionHasBeenUsed" xlink:label="ifrs-full_ExpenseRelatingToShorttermLeasesForWhichRecognitionExemptionHasBeenUsed_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_ExpenseRelatingToShorttermLeasesForWhichRecognitionExemptionHasBeenUsed_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CashOutflowForLeases" xlink:label="ifrs-full_CashOutflowForLeases_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_CashOutflowForLeases_639089076754154299" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AdditionsOtherThanThroughBusinessCombinationsRightofuseAssets" xlink:label="ifrs-full_AdditionsOtherThanThroughBusinessCombinationsRightofuseAssets_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_AdditionsOtherThanThroughBusinessCombinationsRightofuseAssets_639089076754154299" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LeasesTerm" xlink:label="prqr_LeasesTerm_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_LeasesTerm_639089076754154299" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LeasesExtensionTerm" xlink:label="prqr_LeasesExtensionTerm_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_LeasesExtensionTerm_639089076754154299" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInLeaseLiabilitiesThroughModificationsAndAmendments" xlink:label="prqr_IncreaseDecreaseInLeaseLiabilitiesThroughModificationsAndAmendments_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_IncreaseDecreaseInLeaseLiabilitiesThroughModificationsAndAmendments_639089076754154299" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseInRightOfUseAssetThroughModificationOfLeaseTerms" xlink:label="prqr_IncreaseInRightOfUseAssetThroughModificationOfLeaseTerms_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_IncreaseInRightOfUseAssetThroughModificationOfLeaseTerms_639089076754154299" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseDecreaseInLeaseLiabilitiesThroughRemeasurement" xlink:label="prqr_IncreaseDecreaseInLeaseLiabilitiesThroughRemeasurement_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_IncreaseDecreaseInLeaseLiabilitiesThroughRemeasurement_639089076754154299" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IncreaseInRightOfUseAssetThroughRemeasurementOfLeaseLiability" xlink:label="prqr_IncreaseInRightOfUseAssetThroughRemeasurementOfLeaseLiability_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="prqr_IncreaseInRightOfUseAssetThroughRemeasurementOfLeaseLiability_639089076754154299" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_GrossLeaseLiabilities" xlink:label="ifrs-full_GrossLeaseLiabilities_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639089076754154299" xlink:to="ifrs-full_GrossLeaseLiabilities_639089076754154299" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCommitmentsAndContingenciesClaimsAndPatentLicenseAgreementDetails" xlink:type="extended" xlink:title="99942501 - Disclosure - Commitments and Contingencies - Claims and Patent License Agreement (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesAbstract" xlink:label="DisclosureOfContingentLiabilitiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesTable" xlink:label="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfContingentLiabilitiesAbstract" xlink:to="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis" xlink:label="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain" xlink:label="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" xlink:to="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AgreementWithIonisPharmaceuticalsToLicenseQr1123Member" xlink:label="prqr_AgreementWithIonisPharmaceuticalsToLicenseQr1123Member_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" xlink:to="prqr_AgreementWithIonisPharmaceuticalsToLicenseQr1123Member_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesLineItems" xlink:label="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CollaborativeArrangementUpfrontPaymentMadeInOrdinarySharesToCounterparty" xlink:label="prqr_CollaborativeArrangementUpfrontPaymentMadeInOrdinarySharesToCounterparty_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_CollaborativeArrangementUpfrontPaymentMadeInOrdinarySharesToCounterparty_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CollaborativeArrangementPricePerSharePaidToCounterparty" xlink:label="prqr_CollaborativeArrangementPricePerSharePaidToCounterparty_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_CollaborativeArrangementPricePerSharePaidToCounterparty_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CollaborationAgreementPremiumOnSharePricePaid" xlink:label="prqr_CollaborationAgreementPremiumOnSharePricePaid_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_CollaborationAgreementPremiumOnSharePricePaid_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_CollaborationAgreementMeasurementPeriodForVolumeWeightedAveragePricePerShare" xlink:label="prqr_CollaborationAgreementMeasurementPeriodForVolumeWeightedAveragePricePerShare_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_CollaborationAgreementMeasurementPeriodForVolumeWeightedAveragePricePerShare_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_IssueOfEquity" xlink:label="ifrs-full_IssueOfEquity_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="ifrs-full_IssueOfEquity_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ProportionOfOwnershipInterestInAssociate" xlink:label="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="ifrs-full_ProportionOfOwnershipInterestInAssociate_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_LossContingencyClaimsNumber" xlink:label="prqr_LossContingencyClaimsNumber_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_LossContingencyClaimsNumber_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCommitmentsAndContingenciesClinicalSupportAgreementsDetails" xlink:type="extended" xlink:title="99942502 - Disclosure - Commitments and Contingencies - Clinical support agreements (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesAbstract" xlink:label="DisclosureOfContingentLiabilitiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesTable" xlink:label="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfContingentLiabilitiesAbstract" xlink:to="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_RangeAxis_639089076754154299" order="1" use="optional" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076754154299" xlink:to="ifrs-full_RangeDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BottomOfRangeMember" xlink:label="ifrs-full_BottomOfRangeMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076754154299" xlink:to="ifrs-full_BottomOfRangeMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076754154299" xlink:to="ifrs-full_TopOfRangeMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityAxis" xlink:label="ifrs-full_MaturityAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_MaturityAxis_639089076754154299" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_MaturityDomain" xlink:label="ifrs-full_MaturityDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityAxis_639089076754154299" xlink:to="ifrs-full_MaturityDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NotLaterThanOneYearMember" xlink:label="ifrs-full_NotLaterThanOneYearMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MaturityDomain_639089076754154299" xlink:to="ifrs-full_NotLaterThanOneYearMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis" xlink:label="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain" xlink:label="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillAxis_639089076754154299" xlink:to="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_UltevursenMember" xlink:label="prqr_UltevursenMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfIntangibleAssetsOtherThanGoodwillDomain_639089076754154299" xlink:to="prqr_UltevursenMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis" xlink:label="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain" xlink:label="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeAxis_639089076754154299" xlink:to="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ClinicalSupportAgreementWithFoundationFightingBlindnessFfbMember" xlink:label="prqr_ClinicalSupportAgreementWithFoundationFightingBlindnessFfbMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" xlink:to="prqr_ClinicalSupportAgreementWithFoundationFightingBlindnessFfbMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ResearchAndDevelopmentAgreementWithRettSyndromeResearchTrustMember" xlink:label="prqr_ResearchAndDevelopmentAgreementWithRettSyndromeResearchTrustMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsCollaborativeArrangementAndArrangementOtherThanCollaborativeDomain_639089076754154299" xlink:to="prqr_ResearchAndDevelopmentAgreementWithRettSyndromeResearchTrustMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfContingentLiabilitiesLineItems" xlink:label="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_FundingReceivedUnderAgreement" xlink:label="prqr_FundingReceivedUnderAgreement_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_FundingReceivedUnderAgreement_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ResearchAndDevelopmentCommitments" xlink:label="prqr_ResearchAndDevelopmentCommitments_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_ResearchAndDevelopmentCommitments_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NoncurrentResearchAndDevelopmentCommitmentsMaturity" xlink:label="prqr_NoncurrentResearchAndDevelopmentCommitmentsMaturity_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_NoncurrentResearchAndDevelopmentCommitmentsMaturity_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ResearchAndDevelopmentCommitmentsRelatedToOngoingClinicalTrial" xlink:label="prqr_ResearchAndDevelopmentCommitmentsRelatedToOngoingClinicalTrial_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_ResearchAndDevelopmentCommitmentsRelatedToOngoingClinicalTrial_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_RepaymentsOfPreviouslyReceivedFunding" xlink:label="prqr_RepaymentsOfPreviouslyReceivedFunding_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_RepaymentsOfPreviouslyReceivedFunding_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfEarnOutPaymentsForMilestonesAndSalesToBeReceived" xlink:label="prqr_PercentageOfEarnOutPaymentsForMilestonesAndSalesToBeReceived_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_PercentageOfEarnOutPaymentsForMilestonesAndSalesToBeReceived_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MaximumGrantReceivableForInitialPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MaximumGrantReceivableForAdditionalPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639089076754154299" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_OneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct" xlink:label="prqr_OneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_OneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfInstallmentsOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct" xlink:label="prqr_NumberOfInstallmentsOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_NumberOfInstallmentsOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PaymentTermOfFirstInstallmentOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct" xlink:label="prqr_PaymentTermOfFirstInstallmentOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_PaymentTermOfFirstInstallmentOfOneTimeMilestonePaymentDueToCounterpartyFollowingFirstCommercialSaleOfProduct_639089076754154299" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_WarrantsEconomicLifetime" xlink:label="prqr_WarrantsEconomicLifetime_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_WarrantsEconomicLifetime_639089076754154299" order="12" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_IfrsClassOfWarrantOrRightNumberOfSecuritiesCalledByWarrantsOrRights_639089076754154299" order="13" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights" xlink:label="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_IfrsClassOfWarrantOrRightExercisePriceOfWarrantsOrRights_639089076754154299" order="14" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccurs" xlink:label="prqr_AmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccurs_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_AmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccurs_639089076754154299" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfTranchesThroughWhichAmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccursWillBeSetOffAgainstMilestonePayment" xlink:label="prqr_NumberOfTranchesThroughWhichAmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccursWillBeSetOffAgainstMilestonePayment_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_NumberOfTranchesThroughWhichAmountThatCounterpartyCanElectToReceiveInLieuOfWarrantsIfChangeOfControlTransactionOccursWillBeSetOffAgainstMilestonePayment_639089076754154299" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PercentageOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram" xlink:label="prqr_PercentageOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_PercentageOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram_639089076754154299" order="17" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_PaymentTermFromReceiptOfLicensingRevenueOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram" xlink:label="prqr_PaymentTermFromReceiptOfLicensingRevenueOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfContingentLiabilitiesLineItems_639089076754154299" xlink:to="prqr_PaymentTermFromReceiptOfLicensingRevenueOfRoyaltiesPayableToCounterpartyIfEntityLicensesOutProgram_639089076754154299" order="18" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsCompensationDetails" xlink:type="extended" xlink:title="99942601 - Disclosure - Related-Party Transactions - Compensation (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:label="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable" xlink:label="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:to="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CategoriesOfRelatedPartiesAxis" xlink:label="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CategoriesOfRelatedPartiesDomain" xlink:label="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" xlink:to="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NonExecutiveDirectorsMember" xlink:label="prqr_NonExecutiveDirectorsMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" xlink:to="prqr_NonExecutiveDirectorsMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.DinkoValerioMember" xlink:label="prqr_Mr.DinkoValerioMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.DinkoValerioMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.AlisonLawtonMember" xlink:label="prqr_Ms.AlisonLawtonMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.AlisonLawtonMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.JamesShannonMember" xlink:label="prqr_Mr.JamesShannonMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.JamesShannonMember_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.BartFiliusMember" xlink:label="prqr_Mr.BartFiliusMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.BartFiliusMember_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.BegonaCarrenoMember" xlink:label="prqr_Ms.BegonaCarrenoMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.BegonaCarrenoMember_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.TheresaHeggieMember" xlink:label="prqr_Ms.TheresaHeggieMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.TheresaHeggieMember_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MartinMaierMember" xlink:label="prqr_MartinMaierMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_MartinMaierMember_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ExecutiveDirectorsMember" xlink:label="prqr_ExecutiveDirectorsMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" xlink:to="prqr_ExecutiveDirectorsMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.D.a.DeBoerMember" xlink:label="prqr_Mr.D.a.DeBoerMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.D.a.DeBoerMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.R.k.BeukemaMember" xlink:label="prqr_Mr.R.k.BeukemaMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.R.k.BeukemaMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GerardPlatenburgMember" xlink:label="prqr_GerardPlatenburgMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_GerardPlatenburgMember_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_SeniorManagementMember" xlink:label="prqr_SeniorManagementMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" xlink:to="prqr_SeniorManagementMember_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GerardPlatenburgInSeniorManagementRoleMember" xlink:label="prqr_GerardPlatenburgInSeniorManagementRoleMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_SeniorManagementMember_639089076754154299" xlink:to="prqr_GerardPlatenburgInSeniorManagementRoleMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems" xlink:label="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_KeyManagementPersonnelCompensationShorttermEmployeeBenefits" xlink:label="ifrs-full_KeyManagementPersonnelCompensationShorttermEmployeeBenefits_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_KeyManagementPersonnelCompensationShorttermEmployeeBenefits_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_KeyManagementPersonnelCompensationPostemploymentBenefits" xlink:label="ifrs-full_KeyManagementPersonnelCompensationPostemploymentBenefits_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_KeyManagementPersonnelCompensationPostemploymentBenefits_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_KeyManagementPersonnelCompensationTerminationBenefits" xlink:label="ifrs-full_KeyManagementPersonnelCompensationTerminationBenefits_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_KeyManagementPersonnelCompensationTerminationBenefits_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_KeyManagementPersonnelCompensationSharebasedPayment" xlink:label="ifrs-full_KeyManagementPersonnelCompensationSharebasedPayment_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_KeyManagementPersonnelCompensationSharebasedPayment_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_KeyManagementPersonnelCompensation" xlink:label="ifrs-full_KeyManagementPersonnelCompensation_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_KeyManagementPersonnelCompensation_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized" xlink:label="prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRelatedPartyTransactionsStockOptionsDetails" xlink:type="extended" xlink:title="99942602 - Disclosure - Related-Party Transactions - Stock options (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:label="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable" xlink:label="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:to="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" order="1" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2025/elts/srt-2025.xsd#srt_StatementScenarioAxis" xlink:label="srt_StatementScenarioAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="srt_StatementScenarioAxis_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2025/elts/srt-2025.xsd#srt_ScenarioUnspecifiedDomain" xlink:label="srt_ScenarioUnspecifiedDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_StatementScenarioAxis_639089076754154299" xlink:to="srt_ScenarioUnspecifiedDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScenarioOneMember" xlink:label="prqr_ScenarioOneMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ScenarioUnspecifiedDomain_639089076754154299" xlink:to="prqr_ScenarioOneMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ScenarioTwoMember" xlink:label="prqr_ScenarioTwoMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="srt_ScenarioUnspecifiedDomain_639089076754154299" xlink:to="prqr_ScenarioTwoMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeAxis" xlink:label="ifrs-full_RangeAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="ifrs-full_RangeAxis_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_RangeDomain" xlink:label="ifrs-full_RangeDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeAxis_639089076754154299" xlink:to="ifrs-full_RangeDomain_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BottomOfRangeMember" xlink:label="ifrs-full_BottomOfRangeMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076754154299" xlink:to="ifrs-full_BottomOfRangeMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_TopOfRangeMember" xlink:label="ifrs-full_TopOfRangeMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RangeDomain_639089076754154299" xlink:to="ifrs-full_TopOfRangeMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CategoriesOfRelatedPartiesAxis" xlink:label="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_CategoriesOfRelatedPartiesDomain" xlink:label="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesAxis_639089076754154299" xlink:to="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NonExecutiveDirectorsMember" xlink:label="prqr_NonExecutiveDirectorsMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" xlink:to="prqr_NonExecutiveDirectorsMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.DinkoValerioMember" xlink:label="prqr_Mr.DinkoValerioMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.DinkoValerioMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.AlisonLawtonMember" xlink:label="prqr_Ms.AlisonLawtonMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.AlisonLawtonMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.JamesShannonMember" xlink:label="prqr_Mr.JamesShannonMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.JamesShannonMember_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.BartFiliusMember" xlink:label="prqr_Mr.BartFiliusMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.BartFiliusMember_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.BegonaCarrenoMember" xlink:label="prqr_Ms.BegonaCarrenoMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.BegonaCarrenoMember_639089076754154299" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Ms.TheresaHeggieMember" xlink:label="prqr_Ms.TheresaHeggieMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Ms.TheresaHeggieMember_639089076754154299" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_MartinMaierMember" xlink:label="prqr_MartinMaierMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_NonExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_MartinMaierMember_639089076754154299" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_ExecutiveDirectorsMember" xlink:label="prqr_ExecutiveDirectorsMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CategoriesOfRelatedPartiesDomain_639089076754154299" xlink:to="prqr_ExecutiveDirectorsMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.D.a.DeBoerMember" xlink:label="prqr_Mr.D.a.DeBoerMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.D.a.DeBoerMember_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_Mr.R.k.BeukemaMember" xlink:label="prqr_Mr.R.k.BeukemaMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_Mr.R.k.BeukemaMember_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_GerardPlatenburgMember" xlink:label="prqr_GerardPlatenburgMember_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ExecutiveDirectorsMember_639089076754154299" xlink:to="prqr_GerardPlatenburgMember_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems" xlink:label="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesTable_639089076754154299" xlink:to="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfSharesOutstanding" xlink:label="ifrs-full_NumberOfSharesOutstanding_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_NumberOfSharesOutstanding_639089076754154299" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfOutstandingShareOptions" xlink:label="ifrs-full_NumberOfOutstandingShareOptions_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_NumberOfOutstandingShareOptions_639089076754154299" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement" xlink:label="ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement_639089076754154299" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_NumberOfShareOptionsGrantedInSharebasedPaymentArrangement_639089076754154299" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_ExercisePriceShareOptionsGranted2019" xlink:label="ifrs-full_ExercisePriceShareOptionsGranted2019_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_ExercisePriceShareOptionsGranted2019_639089076754310898" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfShareOptionsGrantedThatAreSubjectToNonMarketPerformanceConditions" xlink:label="prqr_NumberOfShareOptionsGrantedThatAreSubjectToNonMarketPerformanceConditions_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_NumberOfShareOptionsGrantedThatAreSubjectToNonMarketPerformanceConditions_639089076754310898" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfTranches" xlink:label="prqr_NumberOfTranches_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_NumberOfTranches_639089076754310898" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate" xlink:label="prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_NumberOfRemainingTranchesAfterFirstAnniversaryOfGrantDate_639089076754310898" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_VestingPercentagePerTranche" xlink:label="prqr_VestingPercentagePerTranche_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_VestingPercentagePerTranche_639089076754310898" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized" xlink:label="prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="prqr_KeyManagementPersonnelCompensationShortTermEmployeeBenefitsBonusBasedOnGoalsRealized_639089076754310898" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_BorrowingsInterestRate" xlink:label="ifrs-full_BorrowingsInterestRate_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_BorrowingsInterestRate_639089076754310898" order="10" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019" xlink:label="ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTransactionsBetweenRelatedPartiesLineItems_639089076754154299" xlink:to="ifrs-full_WeightedAverageRemainingContractualLifeOfOutstandingShareOptions2019_639089076754310898" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureAuditorFeesDetails" xlink:type="extended" xlink:title="99942701 - Disclosure - Auditor fees (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AuditorsRemunerationAbstract" xlink:label="AuditorsRemunerationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AuditorsRemunerationForAuditServices" xlink:label="ifrs-full_AuditorsRemunerationForAuditServices_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="AuditorsRemunerationAbstract" xlink:to="ifrs-full_AuditorsRemunerationForAuditServices_639089076754310898" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20251231.xsd#prqr_AuditorsRemunerationForAuditRelatedFees" xlink:label="prqr_AuditorsRemunerationForAuditRelatedFees_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="AuditorsRemunerationAbstract" xlink:to="prqr_AuditorsRemunerationForAuditRelatedFees_639089076754310898" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_AuditorsRemuneration" xlink:label="ifrs-full_AuditorsRemuneration_639089076754310898" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="AuditorsRemunerationAbstract" xlink:to="ifrs-full_AuditorsRemuneration_639089076754310898" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://xbrl.sec.gov/ecd/role/InsiderTradingPoliciesProc" xlink:type="extended" xlink:title="995447 - Disclosure - Insider Trading Policies and Procedures" xmlns="http://www.xbrl.org/2003/linkbase" />
  <presentationLink xlink:role="http://xbrl.sec.gov/cyd/role/CybersecurityRiskManagementAndStrategyDisclosure" xlink:type="extended" xlink:title="995550 - Disclosure - Cybersecurity Risk Management and Strategy Disclosure" xmlns="http://www.xbrl.org/2003/linkbase" />
</link:linkbase>
