<?xml version="1.0" encoding="utf-8"?>
<!--XBRL document created with Toppan Merrill Bridge  11.3.0.1 -->
<!--Based on XBRL 2.1-->
<!--Created on: 5/12/2026 7:03:09 AM-->
<!--Modified on: 5/12/2026 7:03:09 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-20260331.xsd#DocumentDocumentAndEntityInformation" roleURI="http://www.proqr.com/role/DocumentDocumentAndEntityInformation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#StatementCondensedConsolidatedStatementOfFinancialPosition" roleURI="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfFinancialPosition" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#StatementCondensedConsolidatedStatementOfProfitOrLossAndOtherComprehensiveIncome" roleURI="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfProfitOrLossAndOtherComprehensiveIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#StatementCondensedConsolidatedStatementOfChangesInEquity" roleURI="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfChangesInEquity" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#StatementCondensedConsolidatedStatementOfCashFlows" roleURI="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfCashFlows" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureGeneralInformation" roleURI="http://www.proqr.com/role/DisclosureGeneralInformation" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureSignificantAccountingPolicies" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPolicies" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureAdoptionOfNewAndRevisedInternationalFinancialReportingStandards" roleURI="http://www.proqr.com/role/DisclosureAdoptionOfNewAndRevisedInternationalFinancialReportingStandards" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureCriticalAccountingEstimatesAndJudgements" roleURI="http://www.proqr.com/role/DisclosureCriticalAccountingEstimatesAndJudgements" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureCashAndCashEquivalents" roleURI="http://www.proqr.com/role/DisclosureCashAndCashEquivalents" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureTradeAndOtherReceivables" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosurePropertyPlantAndEquipment" roleURI="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipment" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherCurrentLiabilities" roleURI="http://www.proqr.com/role/DisclosureOtherCurrentLiabilities" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureBorrowings" roleURI="http://www.proqr.com/role/DisclosureBorrowings" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureLeaseLiabilities" roleURI="http://www.proqr.com/role/DisclosureLeaseLiabilities" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureDeferredIncome" roleURI="http://www.proqr.com/role/DisclosureDeferredIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureShareholdersEquity" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquity" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureRevenue" roleURI="http://www.proqr.com/role/DisclosureRevenue" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherIncome" roleURI="http://www.proqr.com/role/DisclosureOtherIncome" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureResearchAndDevelopmentCosts" roleURI="http://www.proqr.com/role/DisclosureResearchAndDevelopmentCosts" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureGeneralAndAdministrativeCosts" roleURI="http://www.proqr.com/role/DisclosureGeneralAndAdministrativeCosts" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureInvestmentsInFinancialAssets" roleURI="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssets" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureIncomeTaxes" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxes" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureRelatedPartyTransactions" roleURI="http://www.proqr.com/role/DisclosureRelatedPartyTransactions" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureEventsAfterBalanceSheetDate" roleURI="http://www.proqr.com/role/DisclosureEventsAfterBalanceSheetDate" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureSignificantAccountingPoliciesPolicies" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesPolicies" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureTradeAndOtherReceivablesTables" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureBorrowingsTables" roleURI="http://www.proqr.com/role/DisclosureBorrowingsTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureDeferredIncomeTables" roleURI="http://www.proqr.com/role/DisclosureDeferredIncomeTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherIncomeTables" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeTables" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureGeneralInformationDetails" roleURI="http://www.proqr.com/role/DisclosureGeneralInformationDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureSignificantAccountingPoliciesDetails" roleURI="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureCriticalAccountingEstimatesAndJudgementsDetails" roleURI="http://www.proqr.com/role/DisclosureCriticalAccountingEstimatesAndJudgementsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureCashAndCashEquivalentsDetails" roleURI="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureTradeAndOtherReceivablesDetails" roleURI="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosurePropertyPlantAndEquipmentDetails" roleURI="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherCurrentLiabiltiesDetails" roleURI="http://www.proqr.com/role/DisclosureOtherCurrentLiabiltiesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureBorrowingsDetails" roleURI="http://www.proqr.com/role/DisclosureBorrowingsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureLeaseLiabilitiesDetails" roleURI="http://www.proqr.com/role/DisclosureLeaseLiabilitiesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureDeferredIncomeDetails" roleURI="http://www.proqr.com/role/DisclosureDeferredIncomeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureShareholdersEquityShareCapitalDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityShareCapitalDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureShareholdersEquitySaleOfSharesDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquitySaleOfSharesDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureShareholdersEquityShareOptionsDetails" roleURI="http://www.proqr.com/role/DisclosureShareholdersEquityShareOptionsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureRevenueDetails" roleURI="http://www.proqr.com/role/DisclosureRevenueDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherIncomeDetails" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureOtherIncomeNarrativeDetails" roleURI="http://www.proqr.com/role/DisclosureOtherIncomeNarrativeDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureResearchAndDevelopmentCostsDetails" roleURI="http://www.proqr.com/role/DisclosureResearchAndDevelopmentCostsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureGeneralAndAdministrativeCostsDetails" roleURI="http://www.proqr.com/role/DisclosureGeneralAndAdministrativeCostsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureInvestmentsInFinancialAssetsDetails" roleURI="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssetsDetails" xmlns="http://www.xbrl.org/2003/linkbase" />
  <roleRef xlink:type="simple" xlink:href="prqr-20260331.xsd#DisclosureIncomeTaxesDetails" roleURI="http://www.proqr.com/role/DisclosureIncomeTaxesDetails" 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="00090 - Document - Document and Entity Information" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DocumentAndEntityInformationAbstract" xlink:label="DocumentAndEntityInformationAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentType" xlink:label="dei_DocumentType_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentType_639141661886023465" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentPeriodEndDate" xlink:label="dei_DocumentPeriodEndDate_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentPeriodEndDate_639141661886023465" order="2" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_CurrentFiscalYearEndDate" xlink:label="dei_CurrentFiscalYearEndDate_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_CurrentFiscalYearEndDate_639141661886023465" order="3" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityRegistrantName" xlink:label="dei_EntityRegistrantName_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_EntityRegistrantName_639141661886023465" order="4" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentFiscalYearFocus" xlink:label="dei_DocumentFiscalYearFocus_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentFiscalYearFocus_639141661886023465" order="5" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_DocumentFiscalPeriodFocus" xlink:label="dei_DocumentFiscalPeriodFocus_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_DocumentFiscalPeriodFocus_639141661886023465" order="6" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_EntityCentralIndexKey" xlink:label="dei_EntityCentralIndexKey_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_EntityCentralIndexKey_639141661886023465" order="7" use="optional" />
    <loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2025/dei-2025.xsd#dei_AmendmentFlag" xlink:label="dei_AmendmentFlag_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DocumentAndEntityInformationAbstract" xlink:to="dei_AmendmentFlag_639141661886023465" order="8" use="optional" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfFinancialPosition" xlink:type="extended" xlink:title="00100 - Statement - Condensed 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfFinancialPositionAbstract" xlink:to="ifrs-full_AssetsAbstract_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_PropertyPlantAndEquipmentIncludingRightofuseAssets_639141661886023465" 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_NoncurrentAssets" xlink:label="ifrs-full_NoncurrentAssets_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_NoncurrentAssets_639141661886023465" order="2" 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_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_CashAndCashEquivalents_639141661886023465" 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_TradeAndOtherCurrentReceivables" xlink:label="ifrs-full_TradeAndOtherCurrentReceivables_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_TradeAndOtherCurrentReceivables_639141661886023465" 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_CurrentReceivablesFromTaxesOtherThanIncomeTax" xlink:label="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_CurrentReceivablesFromTaxesOtherThanIncomeTax_639141661886023465" 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_CurrentAssets" xlink:label="ifrs-full_CurrentAssets_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_CurrentAssets_639141661886023465" order="6" 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_Assets" xlink:label="ifrs-full_Assets_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AssetsAbstract_639141661886023465" xlink:to="ifrs-full_Assets_639141661886023465" 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_EquityAndLiabilitiesAbstract" xlink:label="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfFinancialPositionAbstract" xlink:to="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_EquityAbstract_639141661886023465" 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_EquityAttributableToOwnersOfParent" xlink:label="ifrs-full_EquityAttributableToOwnersOfParent_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639141661886023465" xlink:to="ifrs-full_EquityAttributableToOwnersOfParent_639141661886023465" 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_Equity" xlink:label="ifrs-full_Equity_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAbstract_639141661886023465" xlink:to="ifrs-full_Equity_639141661886023465" order="2" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_LiabilitiesAbstract_639141661886023465" 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_NoncurrentLeaseLiabilities" xlink:label="ifrs-full_NoncurrentLeaseLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_NoncurrentLeaseLiabilities_639141661886023465" 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_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities" xlink:label="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639141661886023465" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" 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_NoncurrentLiabilities" xlink:label="ifrs-full_NoncurrentLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_NoncurrentLiabilities_639141661886023465" 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_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings" xlink:label="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639141661886023465" 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_CurrentLeaseLiabilities" xlink:label="ifrs-full_CurrentLeaseLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_CurrentLeaseLiabilities_639141661886023465" 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_CurrentDerivativeFinancialLiabilities" xlink:label="ifrs-full_CurrentDerivativeFinancialLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_CurrentDerivativeFinancialLiabilities_639141661886023465" 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_TradeAndOtherCurrentPayables" xlink:label="ifrs-full_TradeAndOtherCurrentPayables_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_TradeAndOtherCurrentPayables_639141661886023465" 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_CurrentDeferredIncomeIncludingCurrentContractLiabilities" xlink:label="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_OtherCurrentLiabilities_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_LiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_CurrentLiabilities_639141661886023465" order="10" 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_Liabilities" xlink:label="ifrs-full_Liabilities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_Liabilities_639141661886023465" order="3" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EquityAndLiabilitiesAbstract_639141661886023465" xlink:to="ifrs-full_EquityAndLiabilities_639141661886023465" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="5" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfProfitOrLossAndOtherComprehensiveIncome" xlink:type="extended" xlink:title="00200 - Statement - Condensed Consolidated Statement of Profit or Loss and Other 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_RevenueFromContractsWithCustomers_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OtherIncome_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ResearchAndDevelopmentExpense_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GeneralAndAdministrativeExpense_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OperatingExpense_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossFromOperatingActivities_639141661886023465" 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_FinanceIncomeCost" xlink:label="ifrs-full_FinanceIncomeCost_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_FinanceIncomeCost_639141661886023465" order="7" 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_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss" xlink:label="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_GainsLossesOnFinancialLiabilitiesAtFairValueThroughProfitOrLoss_639141661886023465" 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_ProfitLossBeforeTax" xlink:label="ifrs-full_ProfitLossBeforeTax_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossBeforeTax_639141661886023465" order="9" 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_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLoss_639141661886023465" order="10" 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_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation" xlink:label="ifrs-full_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_OtherComprehensiveIncomeNetOfTaxExchangeDifferencesOnTranslation_639141661886023465" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" 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_ComprehensiveIncome" xlink:label="ifrs-full_ComprehensiveIncome_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ComprehensiveIncome_639141661886023465" order="12" 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_ProfitLossAttributableToAbstract" xlink:label="ifrs-full_ProfitLossAttributableToAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ProfitLossAttributableToAbstract_639141661886023465" 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_ProfitLossAttributableToOwnersOfParent" xlink:label="ifrs-full_ProfitLossAttributableToOwnersOfParent_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProfitLossAttributableToAbstract_639141661886023465" xlink:to="ifrs-full_ProfitLossAttributableToOwnersOfParent_639141661886023465" 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_ComprehensiveIncomeAttributableToAbstract" xlink:label="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639141661886023465" order="14" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComprehensiveIncomeAttributableToAbstract_639141661886023465" xlink:to="ifrs-full_ComprehensiveIncomeAttributableToOwnersOfParent_639141661886023465" 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_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract" xlink:label="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639141661886023465" 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_WeightedAverageShares" xlink:label="ifrs-full_WeightedAverageShares_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639141661886023465" xlink:to="ifrs-full_WeightedAverageShares_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_WeightedAverageSharesAndAdjustedWeightedAverageSharesAbstract_639141661886023465" xlink:to="ifrs-full_AdjustedWeightedAverageShares_639141661886023465" 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_EarningsPerShareAbstract" xlink:label="ifrs-full_EarningsPerShareAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfComprehensiveIncomeAbstract" xlink:to="ifrs-full_EarningsPerShareAbstract_639141661886023465" order="16" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EarningsPerShareAbstract_639141661886023465" xlink:to="ifrs-full_BasicEarningsLossPerShare_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_EarningsPerShareAbstract_639141661886023465" xlink:to="ifrs-full_DilutedEarningsLossPerShare_639141661886023465" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfChangesInEquity" xlink:type="extended" xlink:title="00300 - Statement - Condensed 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfChangesInEquityAbstract" xlink:to="ifrs-full_StatementOfChangesInEquityTable_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityTable_639141661886023465" xlink:to="ifrs-full_ComponentsOfEquityAxis_639141661886023465" 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_IssuedCapitalMember" xlink:label="ifrs-full_IssuedCapitalMember_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_IssuedCapitalMember_639141661886023465" 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_SharePremiumMember" xlink:label="ifrs-full_SharePremiumMember_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_SharePremiumMember_639141661886023465" 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_ReserveOfSharebasedPaymentsMember" xlink:label="ifrs-full_ReserveOfSharebasedPaymentsMember_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_ReserveOfSharebasedPaymentsMember_639141661886023465" 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_ReserveOfExchangeDifferencesOnTranslationMember" xlink:label="ifrs-full_ReserveOfExchangeDifferencesOnTranslationMember_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_ReserveOfExchangeDifferencesOnTranslationMember_639141661886023465" 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_RetainedEarningsMember" xlink:label="ifrs-full_RetainedEarningsMember_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_RetainedEarningsMember_639141661886023465" 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_ComponentsOfEquityDomain" xlink:label="ifrs-full_ComponentsOfEquityDomain_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ComponentsOfEquityAxis_639141661886023465" xlink:to="ifrs-full_ComponentsOfEquityDomain_639141661886023465" order="6" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityTable_639141661886023465" xlink:to="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_Equity_639141661886023465" 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_NumberOfSharesOutstanding" xlink:label="ifrs-full_NumberOfSharesOutstanding_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_NumberOfSharesOutstanding_639141661886023465" order="2" 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_ProfitLoss" xlink:label="ifrs-full_ProfitLoss_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_ProfitLoss_639141661886023465" 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_OtherComprehensiveIncome" xlink:label="ifrs-full_OtherComprehensiveIncome_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_OtherComprehensiveIncome_639141661886023465" order="4" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_IncreaseDecreaseThroughSharebasedPaymentTransactions_639141661886023465" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_TreasurySharesTransferred" xlink:label="prqr_TreasurySharesTransferred_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="prqr_TreasurySharesTransferred_639141661886023465" order="6" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_SharesOptionsLapsed" xlink:label="prqr_SharesOptionsLapsed_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="prqr_SharesOptionsLapsed_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_IncreaseDecreaseThroughExerciseOfOptions_639141661886023465" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="5" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsStockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesStockOptionsExercised_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesStockOptionsExercised_639141661886023465" 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_Equity" xlink:label="ifrs-full_Equity_6391416618860234651" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_Equity_6391416618860234651" order="10" 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_NumberOfSharesOutstanding" xlink:label="ifrs-full_NumberOfSharesOutstanding_6391416618860234651" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_StatementOfChangesInEquityLineItems_639141661886023465" xlink:to="ifrs-full_NumberOfSharesOutstanding_6391416618860234651" order="11" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/StatementCondensedConsolidatedStatementOfCashFlows" xlink:type="extended" xlink:title="00400 - Statement - Condensed 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="StatementOfCashFlowsAbstract" xlink:to="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_ProfitLoss_639141661886023465" order="1" 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_AdjustmentsForReconcileProfitLossAbstract" xlink:label="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInOperatingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_AdjustmentsForOtherIncome" xlink:label="prqr_AdjustmentsForOtherIncome_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="prqr_AdjustmentsForOtherIncome_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2009/role/negatedLabel" 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_AdjustmentsForDepreciationExpense" xlink:label="ifrs-full_AdjustmentsForDepreciationExpense_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_AdjustmentsForDepreciationExpense_639141661886023465" 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_AdjustmentsForSharebasedPayments" xlink:label="ifrs-full_AdjustmentsForSharebasedPayments_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_AdjustmentsForSharebasedPayments_639141661886023465" 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_AdjustmentsForFinanceIncomeCost" xlink:label="ifrs-full_AdjustmentsForFinanceIncomeCost_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_AdjustmentsForFinanceIncomeCost_639141661886023465" order="4" 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_AdjustmentsForFairValueGainsLosses" xlink:label="ifrs-full_AdjustmentsForFairValueGainsLosses_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_AdjustmentsForFairValueGainsLosses_639141661886023465" 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_IncreaseDecreaseInWorkingCapital" xlink:label="ifrs-full_IncreaseDecreaseInWorkingCapital_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_IncreaseDecreaseInWorkingCapital_639141661886023465" order="6" 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_CashFlowsFromUsedInOperations" xlink:label="ifrs-full_CashFlowsFromUsedInOperations_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInOperations_639141661886023465" 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_InterestReceivedClassifiedAsOperatingActivities" xlink:label="ifrs-full_InterestReceivedClassifiedAsOperatingActivities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_InterestReceivedClassifiedAsOperatingActivities_639141661886023465" order="8" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_InterestPaidClassifiedAsOperatingActivities_639141661886023465" order="9" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInOperatingActivities_639141661886023465" 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_CashFlowsFromUsedInInvestingActivitiesAbstract" xlink:label="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639141661886023465" 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_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities" xlink:label="ifrs-full_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_PurchaseOfPropertyPlantAndEquipmentClassifiedAsInvestingActivities_639141661886023465" 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_CashFlowsFromUsedInInvestingActivities" xlink:label="ifrs-full_CashFlowsFromUsedInInvestingActivities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInInvestingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInInvestingActivities_639141661886023465" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" 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_CashFlowsFromUsedInFinancingActivitiesAbstract" xlink:label="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639141661886023465" 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_ProceedsFromExerciseOfOptions" xlink:label="ifrs-full_ProceedsFromExerciseOfOptions_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_ProceedsFromExerciseOfOptions_639141661886023465" order="1" 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_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities" xlink:label="ifrs-full_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_PaymentsOfLeaseLiabilitiesClassifiedAsFinancingActivities_639141661886023465" order="2" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CashFlowsFromUsedInFinancingActivitiesAbstract_639141661886023465" xlink:to="ifrs-full_CashFlowsFromUsedInFinancingActivities_639141661886023465" 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_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges" xlink:label="ifrs-full_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_IncreaseDecreaseInCashAndCashEquivalentsBeforeEffectOfExchangeRateChanges_639141661886023465" 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_EffectOfExchangeRateChangesOnCashAndCashEquivalents" xlink:label="ifrs-full_EffectOfExchangeRateChangesOnCashAndCashEquivalents_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_EffectOfExchangeRateChangesOnCashAndCashEquivalents_639141661886023465" 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_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashAndCashEquivalents_639141661886023465" order="15" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodStartLabel" 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_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_6391416618860234651" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AdjustmentsForReconcileProfitLossAbstract_639141661886023465" xlink:to="ifrs-full_CashAndCashEquivalents_6391416618860234651" order="16" use="optional" preferredLabel="http://www.xbrl.org/2003/role/periodEndLabel" priority="5" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureGeneralInformation" xlink:type="extended" xlink:title="10101 - Disclosure - General Information" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_GeneralInformationAbstract" xlink:label="GeneralInformationAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DisclosureOfGeneralInformationExplanatory" xlink:label="prqr_DisclosureOfGeneralInformationExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="GeneralInformationAbstract" xlink:to="prqr_DisclosureOfGeneralInformationExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPolicies" xlink:type="extended" xlink:title="10201 - Disclosure - Significant Accounting Policies" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DisclosureOfMaterialAccountingPolicyInformationExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureAdoptionOfNewAndRevisedInternationalFinancialReportingStandards" xlink:type="extended" xlink:title="10301 - Disclosure - Adoption of New and Revised International Financial Reporting Standards" 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_DisclosureOfInitialApplicationOfStandardsOrInterpretationsAbstract" xlink:label="DisclosureOfInitialApplicationOfStandardsOrInterpretationsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DescriptionOfInitialApplicationOfStandardsOrInterpretations" xlink:label="ifrs-full_DescriptionOfInitialApplicationOfStandardsOrInterpretations_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfInitialApplicationOfStandardsOrInterpretationsAbstract" xlink:to="ifrs-full_DescriptionOfInitialApplicationOfStandardsOrInterpretations_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCriticalAccountingEstimatesAndJudgements" xlink:type="extended" xlink:title="10401 - Disclosure - Critical Accounting Estimates and Judgements" 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_DisclosureOfChangesInAccountingEstimatesAbstract" xlink:label="DisclosureOfChangesInAccountingEstimatesAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfAccountingJudgementsAndEstimatesExplanatory" xlink:label="ifrs-full_DisclosureOfAccountingJudgementsAndEstimatesExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfChangesInAccountingEstimatesAbstract" xlink:to="ifrs-full_DisclosureOfAccountingJudgementsAndEstimatesExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="6" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCashAndCashEquivalents" xlink:type="extended" xlink:title="10501 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_DisclosureOfCashAndCashEquivalentsExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivables" xlink:type="extended" xlink:title="10601 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract" xlink:to="ifrs-full_DisclosureOfTradeAndOtherReceivablesExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipment" xlink:type="extended" xlink:title="10701 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherCurrentLiabilities" xlink:type="extended" xlink:title="10801 - Disclosure - Other Current Liabilities" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherCurrentLiabilitiesAbstract" xlink:to="ifrs-full_DisclosureOfOtherCurrentLiabilitiesExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowings" xlink:type="extended" xlink:title="10901 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfBorrowingsExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureLeaseLiabilities" xlink:type="extended" xlink:title="11001 - Disclosure - Lease Liabilities" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="PresentationOfLeasesForLesseeAbstract" xlink:to="ifrs-full_DisclosureOfLeasesExplanatory_639141661886023465" 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="11101 - Disclosure - Deferred Income" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract" xlink:to="ifrs-full_DisclosureOfDeferredIncomeExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquity" xlink:type="extended" xlink:title="11201 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfShareCapitalReservesAndOtherEquityInterestExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenue" xlink:type="extended" xlink:title="11301 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_RevenueAbstract" xlink:to="ifrs-full_DisclosureOfRevenueExplanatory_639141661886023465" 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="11401 - Disclosure - Other Income" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="ifrs-full_DisclosureOfOtherOperatingIncomeExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="5" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureResearchAndDevelopmentCosts" xlink:type="extended" xlink:title="11501 - Disclosure - Research and Development Costs" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ResearchAndDevelopmentCostsAbstract" xlink:label="prqr_ResearchAndDevelopmentCostsAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfResearchAndDevelopmentExpenseExplanatory" xlink:label="ifrs-full_DisclosureOfResearchAndDevelopmentExpenseExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ResearchAndDevelopmentCostsAbstract" xlink:to="ifrs-full_DisclosureOfResearchAndDevelopmentExpenseExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureGeneralAndAdministrativeCosts" xlink:type="extended" xlink:title="11601 - Disclosure - General and Administrative 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_SellingGeneralAndAdministrativeExpenseAbstract" xlink:label="SellingGeneralAndAdministrativeExpenseAbstract" />
    <loc xlink:type="locator" xlink:href="https://xbrl.ifrs.org/taxonomy/2025-03-27/full_ifrs/full_ifrs-cor_2025-03-27.xsd#ifrs-full_DisclosureOfGeneralAndAdministrativeExpenseExplanatory" xlink:label="ifrs-full_DisclosureOfGeneralAndAdministrativeExpenseExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SellingGeneralAndAdministrativeExpenseAbstract" xlink:to="ifrs-full_DisclosureOfGeneralAndAdministrativeExpenseExplanatory_639141661886023465" 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="11701 - Disclosure - Investments in Financial Assets" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_InvestmentsInFinancialAssetsAbstract" xlink:to="ifrs-full_DisclosureOfFinancialAssetsExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxes" xlink:type="extended" xlink:title="11801 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="MajorComponentsOfTaxExpenseIncomeAbstract" xlink:to="ifrs-full_DisclosureOfIncomeTaxExplanatory_639141661886023465" 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="11901 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfTransactionsBetweenRelatedPartiesAbstract" xlink:to="ifrs-full_DisclosureOfRelatedPartyExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureEventsAfterBalanceSheetDate" xlink:type="extended" xlink:title="12001 - Disclosure - Events After Balance Sheet Date" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfNonadjustingEventsAfterReportingPeriodAbstract" xlink:to="ifrs-full_DisclosureOfEventsAfterReportingPeriodExplanatory_639141661886023465" 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="20202 - Disclosure - Significant Accounting Policies (Policies)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_DescriptionOfAccountingPolicyForRecognitionOfRevenue" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForRecognitionOfRevenue_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForRecognitionOfRevenue_639141661886023465" 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_DescriptionOfAccountingPolicyForResearchAndDevelopmentExpenseExplanatory" xlink:label="ifrs-full_DescriptionOfAccountingPolicyForResearchAndDevelopmentExpenseExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DescriptionOfAccountingPolicyForResearchAndDevelopmentExpenseExplanatory_639141661886023465" 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_DisclosureOfGoingConcernExplanatory" xlink:label="ifrs-full_DisclosureOfGoingConcernExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="ifrs-full_DisclosureOfGoingConcernExplanatory_639141661886023465" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesTables" xlink:type="extended" xlink:title="30603 - 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-20260331.xsd#prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock" xlink:label="prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_1" xlink:to="prqr_DisclosureOfTradeAndOtherReceivablesTableTextBlock_639141661886023465" order="1" 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="30903 - 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsExplanatory_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncomeTables" xlink:type="extended" xlink:title="31103 - Disclosure - Deferred Income (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract_1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ScheduleOfDeferredIncomeTableTextBlock" xlink:label="prqr_ScheduleOfDeferredIncomeTableTextBlock_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_1" xlink:to="prqr_ScheduleOfDeferredIncomeTableTextBlock_639141661886023465" order="1" 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="31403 - Disclosure - Other Income (Tables)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory" xlink:label="prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_DisclosureOfOtherIncomeTableTextBlockExplanatory_639141661886023465" 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="40101 - Disclosure - General Information (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="GeneralInformationAbstract" xlink:to="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639141661886023465" xlink:to="ifrs-full_SignificantInvestmentsInSubsidiariesAxis_639141661886023465" 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_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesAxis_639141661886023465" xlink:to="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsHoldingB.v.Member" xlink:label="prqr_ProqrTherapeuticsHoldingB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsHoldingB.v.Member_639141661886023465" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIB.v.Member" xlink:label="prqr_ProqrTherapeuticsIB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIB.v.Member_639141661886023465" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIiB.v.Member" xlink:label="prqr_ProqrTherapeuticsIiB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIiB.v.Member_639141661886023465" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIiiB.v.Member" xlink:label="prqr_ProqrTherapeuticsIiiB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIiiB.v.Member_639141661886023465" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIvB.v.Member" xlink:label="prqr_ProqrTherapeuticsIvB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIvB.v.Member_639141661886023465" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsVB.v.Member" xlink:label="prqr_ProqrTherapeuticsVB.v.Member_639141661886023465" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsVB.v.Member_639141661886023465" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsViB.v.Member" xlink:label="prqr_ProqrTherapeuticsViB.v.Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsViB.v.Member_639141661886179436" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsViiB.v.Member" xlink:label="prqr_ProqrTherapeuticsViiB.v.Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsViiB.v.Member_639141661886179436" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsViiiB.v.Member" xlink:label="prqr_ProqrTherapeuticsViiiB.v.Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsViiiB.v.Member_639141661886179436" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIxB.v.Member" xlink:label="prqr_ProqrTherapeuticsIxB.v.Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIxB.v.Member_639141661886179436" order="10" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProqrTherapeuticsIInc.Member" xlink:label="prqr_ProqrTherapeuticsIInc.Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_SignificantInvestmentsInSubsidiariesDomain_639141661886023465" xlink:to="prqr_ProqrTherapeuticsIInc.Member_639141661886179436" 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_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems" xlink:label="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesTable_639141661886023465" xlink:to="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639141661886179436" 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_ProportionOfOwnershipInterestInSubsidiary" xlink:label="ifrs-full_ProportionOfOwnershipInterestInSubsidiary_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfSignificantInvestmentsInSubsidiariesLineItems_639141661886179436" xlink:to="ifrs-full_ProportionOfOwnershipInterestInSubsidiary_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureSignificantAccountingPoliciesDetails" xlink:type="extended" xlink:title="40201 - Disclosure - Significant Accounting Policies (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsAccountingPoliciesAbstract" xlink:label="IfrsAccountingPoliciesAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsNumberOfReportableSegments" xlink:label="prqr_IfrsNumberOfReportableSegments_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsAccountingPoliciesAbstract" xlink:to="prqr_IfrsNumberOfReportableSegments_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCriticalAccountingEstimatesAndJudgementsDetails" xlink:type="extended" xlink:title="40401 - Disclosure - Critical Accounting Estimates and Judgements (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_DisclosureOfChangesInAccountingEstimatesAbstract" xlink:label="ifrs-full_DisclosureOfChangesInAccountingEstimatesAbstract" />
    <loc 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfChangesInAccountingEstimatesAbstract" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_CounterpartiesAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639141661886179436" xlink:to="ifrs-full_CounterpartiesDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639141661886179436" xlink:to="prqr_EliLillyAndCompanyMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639141661886179436" 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_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_CashAndCashEquivalents_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureCashAndCashEquivalentsDetails" xlink:type="extended" xlink:title="40501 - 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_CashAndCashEquivalents" xlink:label="ifrs-full_CashAndCashEquivalents_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="CashAndCashEquivalentsAbstract" xlink:to="ifrs-full_CashAndCashEquivalents_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="9" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureTradeAndOtherReceivablesDetails" xlink:type="extended" xlink:title="40601 - 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-20260331.xsd#prqr_CurrentReceivablesFromCollaborationAgreements" xlink:label="prqr_CurrentReceivablesFromCollaborationAgreements_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_TradeAndOtherReceivablesAbstract_2" xlink:to="prqr_CurrentReceivablesFromCollaborationAgreements_639141661886179436" 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_639141661886179436" />
    <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_639141661886179436" 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_639141661886179436" />
    <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_639141661886179436" 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_639141661886179436" />
    <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_639141661886179436" 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_639141661886179436" />
    <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_639141661886179436" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosurePropertyPlantAndEquipmentDetails" xlink:type="extended" xlink:title="40701 - 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfPropertyPlantAndEquipmentAbstract" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639141661886179436" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639141661886179436" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639141661886179436" xlink:to="ifrs-full_LeaseholdImprovementsMember_639141661886179436" 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_DisclosureOfPropertyPlantAndEquipmentLineItems" xlink:label="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639141661886179436" 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_RightofuseAssets" xlink:label="ifrs-full_RightofuseAssets_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfPropertyPlantAndEquipmentLineItems_639141661886179436" xlink:to="ifrs-full_RightofuseAssets_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="2" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherCurrentLiabiltiesDetails" xlink:type="extended" xlink:title="40801 - Disclosure - Other Current Liabilties (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherCurrentLiabilitiesAbstract_1" xlink:to="ifrs-full_OtherCurrentLiabilities_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureBorrowingsDetails" xlink:type="extended" xlink:title="40901 - 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="BorrowingsAbstract" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639141661886179436" xlink:to="ifrs-full_BorrowingsByNameAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameAxis_639141661886179436" xlink:to="ifrs-full_BorrowingsByNameDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_InnovationCreditMember" xlink:label="prqr_InnovationCreditMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_BorrowingsByNameDomain_639141661886179436" xlink:to="prqr_InnovationCreditMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsClassesOfWarrantsOrRightsAxisAxis" xlink:label="prqr_IfrsClassesOfWarrantsOrRightsAxisAxis_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639141661886179436" xlink:to="prqr_IfrsClassesOfWarrantsOrRightsAxisAxis_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ClassesOfWarrantsOrRightsDomain" xlink:label="prqr_ClassesOfWarrantsOrRightsDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsClassesOfWarrantsOrRightsAxisAxis_639141661886179436" xlink:to="prqr_ClassesOfWarrantsOrRightsDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_PontifaxAndKreosWarrantsMember" xlink:label="prqr_PontifaxAndKreosWarrantsMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ClassesOfWarrantsOrRightsDomain_639141661886179436" xlink:to="prqr_PontifaxAndKreosWarrantsMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="ifrs-full_Borrowings_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="ifrs-full_InterestPayable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="ifrs-full_CurrentBorrowingsAndCurrentPortionOfNoncurrentBorrowings_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="ifrs-full_NotionalAmount_639141661886179436" 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_RepaymentsOfBorrowingsClassifiedAsFinancingActivities" xlink:label="ifrs-full_RepaymentsOfBorrowingsClassifiedAsFinancingActivities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="ifrs-full_RepaymentsOfBorrowingsClassifiedAsFinancingActivities_639141661886179436" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_CurrentBorrowingsExcludingAccruedInterest" xlink:label="prqr_CurrentBorrowingsExcludingAccruedInterest_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="prqr_CurrentBorrowingsExcludingAccruedInterest_639141661886179436" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ConditionalWaiverOfDebtTotal" xlink:label="prqr_ConditionalWaiverOfDebtTotal_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="prqr_ConditionalWaiverOfDebtTotal_639141661886179436" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_WarrantsEconomicLifetime" xlink:label="prqr_WarrantsEconomicLifetime_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDetailedInformationAboutBorrowingsLineItems_639141661886179436" xlink:to="prqr_WarrantsEconomicLifetime_639141661886179436" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureLeaseLiabilitiesDetails" xlink:type="extended" xlink:title="41001 - Disclosure - Lease Liabilities (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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="PresentationOfLeasesForLesseeAbstract" xlink:to="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639141661886179436" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentAxis_639141661886179436" xlink:to="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_OfficeAndLaboratoryFacilityMember" xlink:label="prqr_OfficeAndLaboratoryFacilityMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfPropertyPlantAndEquipmentDomain_639141661886179436" xlink:to="prqr_OfficeAndLaboratoryFacilityMember_639141661886179436" 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_GeographicalAreasAxis" xlink:label="ifrs-full_GeographicalAreasAxis_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639141661886179436" xlink:to="ifrs-full_GeographicalAreasAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasAxis_639141661886179436" xlink:to="ifrs-full_GeographicalAreasDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_LeidenNetherlandsMember" xlink:label="prqr_LeidenNetherlandsMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_GeographicalAreasDomain_639141661886179436" xlink:to="prqr_LeidenNetherlandsMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639141661886179436" order="3" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_AreaOfPropertyUnderLease" xlink:label="prqr_AreaOfPropertyUnderLease_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639141661886179436" xlink:to="prqr_AreaOfPropertyUnderLease_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="3" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_LeaseTerm" xlink:label="prqr_LeaseTerm_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639141661886179436" xlink:to="prqr_LeaseTerm_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_LeaseExtensionTerm" xlink:label="prqr_LeaseExtensionTerm_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639141661886179436" xlink:to="prqr_LeaseExtensionTerm_639141661886179436" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_LeaseCurrentExtensionPeriodUnderOption" xlink:label="prqr_LeaseCurrentExtensionPeriodUnderOption_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfQuantitativeInformationAboutRightofuseAssetsLineItems_639141661886179436" xlink:to="prqr_LeaseCurrentExtensionPeriodUnderOption_639141661886179436" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureDeferredIncomeDetails" xlink:type="extended" xlink:title="41101 - Disclosure - Deferred Income (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DeferredIncomeAbstract" xlink:label="prqr_DeferredIncomeAbstract_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_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DeferredIncomeAbstract_4" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_CounterpartiesAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639141661886179436" xlink:to="ifrs-full_CounterpartiesDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639141661886179436" xlink:to="prqr_EliLillyAndCompanyMember_639141661886179436" 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_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems" xlink:label="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" 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_CurrentDeferredIncomeIncludingCurrentContractLiabilities" xlink:label="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_CurrentDeferredIncomeIncludingCurrentContractLiabilities_639141661886179436" 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_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities" xlink:label="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_NoncurrentDeferredIncomeIncludingNoncurrentContractLiabilities_639141661886179436" 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_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639141661886179436" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/totalLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquityShareCapitalDetails" xlink:type="extended" xlink:title="41201 - 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="DisclosureOfClassesOfShareCapitalAbstract" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" xlink:to="ifrs-full_ClassesOfShareCapitalAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalAxis_639141661886179436" xlink:to="ifrs-full_ClassesOfShareCapitalDomain_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalDomain_639141661886179436" xlink:to="ifrs-full_OrdinarySharesMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ClassesOfShareCapitalDomain_639141661886179436" xlink:to="ifrs-full_PreferenceSharesMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" xlink:to="ifrs-full_CounterpartiesAxis_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639141661886179436" xlink:to="ifrs-full_CounterpartiesDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639141661886179436" xlink:to="prqr_EliLillyAndCompanyMember_639141661886179436" 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_DisclosureOfClassesOfShareCapitalLineItems" xlink:label="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_AuthorizedShareCapitalValue" xlink:label="prqr_AuthorizedShareCapitalValue_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_AuthorizedShareCapitalValue_639141661886179436" 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_NumberOfSharesAuthorised" xlink:label="ifrs-full_NumberOfSharesAuthorised_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_NumberOfSharesAuthorised_639141661886179436" 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_NumberOfSharesIssued" xlink:label="ifrs-full_NumberOfSharesIssued_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_NumberOfSharesIssued_639141661886179436" order="3" 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_NumberOfSharesIssuedAndFullyPaid" xlink:label="ifrs-full_NumberOfSharesIssuedAndFullyPaid_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_NumberOfSharesIssuedAndFullyPaid_639141661886179436" 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_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates" xlink:label="ifrs-full_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_SharesInEntityHeldByEntityOrByItsSubsidiariesOrAssociates_639141661886179436" 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_ParValuePerShare" xlink:label="ifrs-full_ParValuePerShare_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_ParValuePerShare_639141661886179436" order="6" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" order="7" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureShareholdersEquitySaleOfSharesDetails" xlink:type="extended" xlink:title="41202 - 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_639141661886179436" />
    <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_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsSaleOfStockAxis" xlink:label="prqr_IfrsSaleOfStockAxis_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" xlink:to="prqr_IfrsSaleOfStockAxis_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsSaleOfStockDomain" xlink:label="prqr_IfrsSaleOfStockDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsSaleOfStockAxis_639141661886179436" xlink:to="prqr_IfrsSaleOfStockDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ShelfRegistrationStatement2024Member" xlink:label="prqr_ShelfRegistrationStatement2024Member_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_IfrsSaleOfStockDomain_639141661886179436" xlink:to="prqr_ShelfRegistrationStatement2024Member_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember" xlink:label="prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639141661886179436" xlink:to="prqr_AtMarketOfferingsWithCantorFitzgeraldAndCoUnderShelfRegistrationStatementMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_October2024UnderwrittenPublicOfferingMember" xlink:label="prqr_October2024UnderwrittenPublicOfferingMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639141661886179436" xlink:to="prqr_October2024UnderwrittenPublicOfferingMember_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember" xlink:label="prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_October2024UnderwrittenPublicOfferingMember_639141661886179436" xlink:to="prqr_UnderwritersOptionInConnectionToOctober2024UnderwrittenPublicOfferingMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember" xlink:label="prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ShelfRegistrationStatement2024Member_639141661886179436" xlink:to="prqr_SharePurchaseAgreementWithEliLillyAndCompanyMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_MaximumOfferingPriceInShelfRegistrationStatement" xlink:label="prqr_MaximumOfferingPriceInShelfRegistrationStatement_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_MaximumOfferingPriceInShelfRegistrationStatement_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement" xlink:label="prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_PercentageOfCommissionPayableForGrossProceedsFromSalesAgreement_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" order="3" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsSaleOfStockPricePerShare" xlink:label="prqr_IfrsSaleOfStockPricePerShare_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_IfrsSaleOfStockPricePerShare_639141661886179436" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DurationOfUnderwritersOption" xlink:label="prqr_DurationOfUnderwritersOption_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_DurationOfUnderwritersOption_639141661886179436" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_NumberOfSharesCallableForOptionsIssued" xlink:label="prqr_NumberOfSharesCallableForOptionsIssued_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_NumberOfSharesCallableForOptionsIssued_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_ProceedsFromIssuingShares_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="ifrs-full_PaymentsForShareIssueCosts_639141661886179436" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_NetProceedsFromIssuingShares" xlink:label="prqr_NetProceedsFromIssuingShares_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_NetProceedsFromIssuingShares_639141661886179436" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_PurchasePriceCapSharePurchaseAgreement" xlink:label="prqr_PurchasePriceCapSharePurchaseAgreement_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalLineItems_639141661886179436" xlink:to="prqr_PurchasePriceCapSharePurchaseAgreement_639141661886179436" 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="41203 - 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_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable" xlink:label="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfClassesOfShareCapitalAbstract_2" xlink:to="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639141661886179436" 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_AttributionOfExpensesByNatureToTheirFunctionAxis" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639141661886179436" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639141661886179436" 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_AttributionOfExpensesByNatureToTheirFunctionDomain" xlink:label="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionAxis_639141661886179436" xlink:to="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsSellingGeneralAndAdministrativeExpensesMember" xlink:label="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639141661886179436" xlink:to="prqr_IfrsSellingGeneralAndAdministrativeExpensesMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsResearchAndDevelopmentExpenseMember" xlink:label="prqr_IfrsResearchAndDevelopmentExpenseMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_AttributionOfExpensesByNatureToTheirFunctionDomain_639141661886179436" xlink:to="prqr_IfrsResearchAndDevelopmentExpenseMember_639141661886179436" 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_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems" xlink:label="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639141661886179436" 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_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets" xlink:label="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfTermsAndConditionsOfSharebasedPaymentArrangementLineItems_639141661886179436" xlink:to="ifrs-full_ExpenseFromEquitysettledSharebasedPaymentTransactionsInWhichGoodsOrServicesReceivedDidNotQualifyForRecognitionAsAssets_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureRevenueDetails" xlink:type="extended" xlink:title="41301 - Disclosure - 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="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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="RevenueAbstract" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_CounterpartiesAxis_639141661886179436" 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_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639141661886179436" xlink:to="ifrs-full_CounterpartiesDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_EliLillyAndCompanyMember" xlink:label="prqr_EliLillyAndCompanyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639141661886179436" xlink:to="prqr_EliLillyAndCompanyMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_ProductsAndServicesAxis_639141661886179436" 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_ProductsAndServicesDomain" xlink:label="ifrs-full_ProductsAndServicesDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesAxis_639141661886179436" xlink:to="ifrs-full_ProductsAndServicesDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_MilestonePaymentsMember" xlink:label="prqr_MilestonePaymentsMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_ProductsAndServicesDomain_639141661886179436" xlink:to="prqr_MilestonePaymentsMember_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersTable_639141661886179436" xlink:to="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" 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_DeferredIncomeIncludingContractLiabilities" xlink:label="ifrs-full_DeferredIncomeIncludingContractLiabilities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_DeferredIncomeIncludingContractLiabilities_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsStockIssuedDuringPeriodSharesNewIssues" xlink:label="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="prqr_IfrsStockIssuedDuringPeriodSharesNewIssues_639141661886179436" 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_NumberOfSharesIssued" xlink:label="ifrs-full_NumberOfSharesIssued_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_NumberOfSharesIssued_639141661886179436" 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_ProceedsFromIssuingShares" xlink:label="ifrs-full_ProceedsFromIssuingShares_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_ProceedsFromIssuingShares_639141661886179436" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DiscountOnIssueOfShares" xlink:label="prqr_DiscountOnIssueOfShares_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="prqr_DiscountOnIssueOfShares_639141661886179436" order="5" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership" xlink:label="prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="prqr_AdditionalConsiderationToBeReceivedIfCounterpartyExercisesOptionToExpandPartnership_639141661886179436" order="6" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_NumberOfPerformanceObligationsInCollaborationAgreement" xlink:label="prqr_NumberOfPerformanceObligationsInCollaborationAgreement_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="prqr_NumberOfPerformanceObligationsInCollaborationAgreement_639141661886179436" 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_ReceiptsFromSalesOfGoodsAndRenderingOfServices" xlink:label="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639141661886179436" order="8" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ValueOfMilestonesReachedDuringPeriod" xlink:label="prqr_ValueOfMilestonesReachedDuringPeriod_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_DisclosureOfDisaggregationOfRevenueFromContractsWithCustomersLineItems_639141661886179436" xlink:to="prqr_ValueOfMilestonesReachedDuringPeriod_639141661886179436" order="9" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureOtherIncomeDetails" xlink:type="extended" xlink:title="41401 - Disclosure - Other Income (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsRevenueFromGrants" xlink:label="prqr_IfrsRevenueFromGrants_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_IfrsRevenueFromGrants_639141661886179436" 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_OtherIncome" xlink:label="ifrs-full_OtherIncome_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="ifrs-full_OtherIncome_639141661886179436" order="2" 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="41402 - Disclosure - Other Income - Narrative (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsOtherIncomeAbstract" xlink:label="IfrsOtherIncomeAbstract" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_OtherIncomeTable" xlink:label="prqr_OtherIncomeTable_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="IfrsOtherIncomeAbstract" xlink:to="prqr_OtherIncomeTable_639141661886179436" 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639141661886179436" xlink:to="ifrs-full_CounterpartiesAxis_639141661886179436" 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_CounterpartiesDomain" xlink:label="ifrs-full_CounterpartiesDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesAxis_639141661886179436" xlink:to="ifrs-full_CounterpartiesDomain_639141661886179436" order="1" use="optional" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_RettSyndromeResearchTrustMember" xlink:label="prqr_RettSyndromeResearchTrustMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_CounterpartiesDomain_639141661886179436" xlink:to="prqr_RettSyndromeResearchTrustMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_OtherIncomeLineItems" xlink:label="prqr_OtherIncomeLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeTable_639141661886179436" xlink:to="prqr_OtherIncomeLineItems_639141661886179436" order="2" use="optional" priority="2" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_IfrsRevenueFromGrants" xlink:label="prqr_IfrsRevenueFromGrants_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639141661886179436" xlink:to="prqr_IfrsRevenueFromGrants_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="4" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_MaximumGrantReceivableForInitialPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639141661886179436" xlink:to="prqr_MaximumGrantReceivableForInitialPhaseOfProject_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_MaximumGrantReceivableForAdditionalPhaseOfProject" xlink:label="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639141661886179436" xlink:to="prqr_MaximumGrantReceivableForAdditionalPhaseOfProject_639141661886179436" 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_ReceiptsFromSalesOfGoodsAndRenderingOfServices" xlink:label="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_OtherIncomeLineItems_639141661886179436" xlink:to="ifrs-full_ReceiptsFromSalesOfGoodsAndRenderingOfServices_639141661886179436" order="4" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureResearchAndDevelopmentCostsDetails" xlink:type="extended" xlink:title="41501 - Disclosure - Research and Development Costs (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ResearchAndDevelopmentCostsAbstract" xlink:label="prqr_ResearchAndDevelopmentCostsAbstract_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_ResearchAndDevelopmentExpense" xlink:label="ifrs-full_ResearchAndDevelopmentExpense_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_ResearchAndDevelopmentCostsAbstract_1" xlink:to="ifrs-full_ResearchAndDevelopmentExpense_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureGeneralAndAdministrativeCostsDetails" xlink:type="extended" xlink:title="41601 - Disclosure - General and Administrative 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_SellingGeneralAndAdministrativeExpenseAbstract" xlink:label="SellingGeneralAndAdministrativeExpenseAbstract" />
    <loc 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_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="SellingGeneralAndAdministrativeExpenseAbstract" xlink:to="ifrs-full_GeneralAndAdministrativeExpense_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/verboseLabel" priority="6" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureInvestmentsInFinancialAssetsDetails" xlink:type="extended" xlink:title="41701 - Disclosure - Investments in Financial Assets (Details)" xmlns="http://www.xbrl.org/2003/linkbase">
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_InvestmentsInFinancialAssetsAbstract" xlink:label="prqr_InvestmentsInFinancialAssetsAbstract_3" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable" xlink:label="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_InvestmentsInFinancialAssetsAbstract_3" xlink:to="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639141661886179436" 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_InvestmentsInEquityInstrumentsMeasuredAtFairValueThroughOtherComprehensiveIncomeAxis" xlink:label="ifrs-full_InvestmentsInEquityInstrumentsMeasuredAtFairValueThroughOtherComprehensiveIncomeAxis_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639141661886179436" xlink:to="ifrs-full_InvestmentsInEquityInstrumentsMeasuredAtFairValueThroughOtherComprehensiveIncomeAxis_639141661886179436" 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_InvestmentsInEquityInstrumentsDesignatedAtFairValueThroughOtherComprehensiveIncomeDomain" xlink:label="ifrs-full_InvestmentsInEquityInstrumentsDesignatedAtFairValueThroughOtherComprehensiveIncomeDomain_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_InvestmentsInEquityInstrumentsMeasuredAtFairValueThroughOtherComprehensiveIncomeAxis_639141661886179436" xlink:to="ifrs-full_InvestmentsInEquityInstrumentsDesignatedAtFairValueThroughOtherComprehensiveIncomeDomain_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_PhoenicisTherapeuticsIncMember" xlink:label="prqr_PhoenicisTherapeuticsIncMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_InvestmentsInEquityInstrumentsDesignatedAtFairValueThroughOtherComprehensiveIncomeDomain_639141661886179436" xlink:to="prqr_PhoenicisTherapeuticsIncMember_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/terseLabel" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_YarrowBiotechnologyMember" xlink:label="prqr_YarrowBiotechnologyMember_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_InvestmentsInEquityInstrumentsDesignatedAtFairValueThroughOtherComprehensiveIncomeDomain_639141661886179436" xlink:to="prqr_YarrowBiotechnologyMember_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems" xlink:label="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateTable_639141661886179436" xlink:to="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" />
    <loc xlink:type="locator" xlink:href="prqr-20260331.xsd#prqr_ProportionOfOwnershipInterest" xlink:label="prqr_ProportionOfOwnershipInterest_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639141661886179436" xlink:to="prqr_ProportionOfOwnershipInterest_639141661886179436" 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_FinancialAssetsAtFairValueThroughOtherComprehensiveIncome" xlink:label="ifrs-full_FinancialAssetsAtFairValueThroughOtherComprehensiveIncome_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="prqr_DisclosureOfInvestmentInFinancialAssetAndGainOnDisposalOfAssociateLineItems_639141661886179436" xlink:to="ifrs-full_FinancialAssetsAtFairValueThroughOtherComprehensiveIncome_639141661886179436" order="2" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
  <presentationLink xlink:role="http://www.proqr.com/role/DisclosureIncomeTaxesDetails" xlink:type="extended" xlink:title="41801 - 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="ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract_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_CurrentTaxLiabilities" xlink:label="ifrs-full_CurrentTaxLiabilities_639141661886179436" />
    <presentationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/parent-child" xlink:from="ifrs-full_MajorComponentsOfTaxExpenseIncomeAbstract_1" xlink:to="ifrs-full_CurrentTaxLiabilities_639141661886179436" order="1" use="optional" preferredLabel="http://www.xbrl.org/2003/role/label" priority="1" />
  </presentationLink>
</link:linkbase>
