UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 6-K

Report of Foreign Private Issuer

Pursuant to Rule 13a-16 or 15d-16 of

the Securities Exchange Act of 1934

For the month of November 2019

Commission File Number: 001-36622

PROQR THERAPEUTICS N.V.

Zernikedreef 9

2333 CK Leiden

The Netherlands

Tel: +31 88 166 7000

(Address, Including ZIP Code, and Telephone Number,
Including Area Code, of Registrant’s Principal Executive Offices)

Indicate by check mark whether the registrant files or will file annual reports under cover of Form 20-F or Form 40-F.

Form 20-F  x  Form 40-F  o

Indicate by check mark if the registrant is submitting the Form 6-K in paper as permitted by Regulation S-T Rule 101(b)(1):  o

Indicate by check mark if the registrant is submitting the Form 6-K in paper as permitted by Regulation S-T Rule 101(b)(7):  o

On November 21, 2019, ProQR Therapeutics N.V. (the “Company”) issued a press release titled, “ProQR Receives Orphan Drug Designation from FDA for QR-1123 for Autosomal Dominant Retinitis Pigmentosa.” A copy of this press release is attached hereto as Exhibit 99.1 and is incorporated herein by reference.

The Company hereby incorporates by reference the information contained herein into the Company’s registration statement on Form F-3 (File No. 333-228251).

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

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INDEX TO EXHIBITS

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Exhibit 99.1

FINAL — FOR RELEASE

ProQR Receives Orphan Drug Designation from FDA for QR-1123 for Autosomal Dominant Retinitis Pigmentosa

LEIDEN, Netherlands & CAMBRIDGE, Mass., Nov. 21, 2019 (GLOBE NEWSWIRE) — ProQR Therapeutics N.V. (Nasdaq:PRQR), a company dedicated to changing lives through the creation of transformative RNA medicines for severe genetic rare diseases, today announced that it received Orphan Drug designation (ODD) from the Food and Drug Administration (FDA) for QR-1123.

QR-1123 is a first-in-class investigational antisense oligonucleotide designed to address the underlying cause of vision loss associated with autosomal dominant retinitis pigmentosa (adRP) due to the P23H mutation in the rhodopsin (RHO) gene.

ODD provides a special status for investigational drugs being developed for rare diseases. The ODD program offers development program tax benefits and a waiver of the NDA application user fee, as well as market exclusivity for up to seven years in the U.S. following market approval.

“We are pleased to have orphan drug designation for our QR-1123 program targeting autosomal dominant retinitis pigmentosa, or adRP,” said Daniel de Boer, Chief Executive Officer of ProQR. “It highlights the unmet need for patients with this progressive disease causing blindness. Our goal is to develop and actively advance a pipeline of programs that can treat inherited retinal diseases like adRP in a targeted manner.”

About QR-1123

QR-1123 is a first-in-class investigational RNA-based oligonucleotide designed to treat adRP due to the P23H mutation in the RHO gene. QR-1123 was discovered and developed by Ionis Pharmaceuticals using Ionis’ proprietary antisense technology. The therapy aims to inhibit the formation of the mutated toxic version of the rhodopsin protein by specifically binding the mutated RHO mRNA. Binding of QR-1123 causes allele specific knockdown of the mutant mRNA by a mechanism called RNase H mediated cleavage without affecting the normal RHO mRNA. QR-1123 is intended to be administered through intravitreal injections in the eye. QR-1123 was in-licensed from Ionis Pharmaceuticals in 2018, and subsequently received IND clearance in August 2019. QR-1123 has received Fast Track designation from the FDA.

About the Phase 1/2 Aurora trial

Aurora, or PQ-1123-001 trial, is a first-in-human study that will initially include up to 35 adults with adRP due to the P23H mutation in the rhodopsin (RHO) gene. The trial will include a single-dose escalation (open label) arm and a multiple-dose (double-masked) arm in which intravitreal injections of QR-1123 or sham procedure will be given in one eye. The objectives of the trial will include evaluation of safety, tolerability, pharmacokinetics and efficacy, as measured by restoration or improvement of visual function and retinal structure through ophthalmic endpoints

such as visual acuity (BCVA), visual field (VF) and optical coherence tomography (OCT). The trial will be conducted at expert sites in North America and is expected to start in 2019.

About adRP

Autosomal dominant retinitis pigmentosa, or adRP, is a severe and rare genetic disease that causes progressive problems in night vision during childhood, leading to visual field loss and frequently resulting in blindness in mid adulthood. In the United States, the most prevalent mutation associated with adRP is the P23H point mutation (also known as the c.68C>A mutation) in the rhodopsin (RHO) gene and affects approximately 2,500 people. This mutation causes misfolding of the rhodopsin protein that becomes toxic to the photoreceptor cells and at the same time diminishes the function of the wild type allele. Over time this results in cell death and progressive vision loss. There are currently no therapies approved or in clinical development for P23H adRP. A natural history study in patients with P23H adRP has been conducted.

About ProQR

ProQR Therapeutics is dedicated to changing lives through the creation of transformative RNA medicines for the treatment of severe genetic rare diseases such as Leber’s congenital amaurosis 10, Usher syndrome and autosomal dominant retinitis pigmentosa. Based on our unique proprietary RNA repair platform technologies we are growing our pipeline with patients and loved ones in mind.

*Since 2012*

FORWARD-LOOKING STATEMENTS

This press release contains forward-looking statements. All statements other than statements of historical fact are forward-looking statements, which are often indicated by terms such as “anticipate,” “believe,” “could,” “estimate,” “expect,” “goal,” “intend,” “look forward to”, “may,” “plan,” “potential,” “predict,” “project,” “should,” “will,” “would” and similar expressions. Forward-looking statements are based on management’s beliefs and assumptions and on information available to management only as of the date of this press release. These forward-looking statements include, but are not limited to, statements regarding QR-1123 and its clinical development and therapeutic potential, including commencement of the Aurora trial, trial design and timing of results from this trial, and the receipt of Orphan Drug designation for QR-1123. Our actual results could differ materially from those anticipated in these forward-looking statements for many reasons, including, without limitation, risks associated with our clinical development activities, including that positive results observed in our prior and ongoing studies may not be replicated in later trials or guarantee approval of any product candidate by regulatory authorities, regulatory review or approval process, that the intended benefits of orphan drug designation for QR-1123 may not be realized, manufacturing processes and facilities, regulatory oversight, product commercialization, intellectual property claims, our ability to maintain our collaboration with Ionis Pharmaceuticals and realize the benefits therefrom, and the risks, uncertainties and other factors in our filings made with the Securities and Exchange Commission, including certain sections of our annual report filed on Form 20-F. Given these risks, uncertainties and other factors, you should not place undue reliance on these forward-looking statements, and we assume no obligation to update these forward-looking statements, even if new information becomes available in the future, except as required by law.

ProQR Therapeutics N.V.

Investor Contact:

Sarah Kiely

ProQR Therapeutics N.V.

T: +1 617 599 6228

skiely@proqr.com

or

Hans Vitzthum

LifeSci Advisors

T: +1 617 535 7743

hans@lifesciadvisors.com

Media Contact:

Sara Zelkovic

LifeSci Public Relations

T: +1 646 876 4933

sara@lifescipublicrelations.com