# EDGAR Filing Document

**Accession Number:** 0001612940
**File Stem:** 0001104659-25-107349
**Filing Date:** 2025-11
**Character Count:** 67823
**Document Hash:** e9babc01e7f46b012994171ced3d6ae2
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0001104659-25-107349.hdr.sgml**: 20251106

**ACCESSION NUMBER**: 0001104659-25-107349

**CONFORMED SUBMISSION TYPE**: 6-K

**PUBLIC DOCUMENT COUNT**: 66

**CONFORMED PERIOD OF REPORT**: 20250930

**FILED AS OF DATE**: 20251106

**DATE AS OF CHANGE**: 20251106

**FILER**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** ProQR Therapeutics N.V.
- **CENTRAL INDEX KEY:** 0001612940
- **STANDARD INDUSTRIAL CLASSIFICATION:** PHARMACEUTICAL PREPARATIONS [2834]
- **ORGANIZATION NAME:** 03 Life Sciences
- **EIN:** 000000000
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** 6-K
- **SEC ACT:** 1934 Act
- **SEC FILE NUMBER:** 001-36622
- **FILM NUMBER:** 251456048

**BUSINESS ADDRESS:**
- **STREET 1:** ZERNIKEDREEF 9
- **CITY:** LEIDEN
- **STATE:** P7
- **ZIP:** 2333 CK
- **BUSINESS PHONE:** 31 88 166 7000

**MAIL ADDRESS:**
- **STREET 1:** ZERNIKEDREEF 9
- **CITY:** LEIDEN
- **STATE:** P7
- **ZIP:** 2333 CK

**FORMER COMPANY:**
- **FORMER CONFORMED NAME:** ProQR Therapeutics B.V.
- **DATE OF NAME CHANGE:** 20140708

------

**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**

**November 6, 2025**

**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 ⌧ Form 40-F ◻

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): ◻

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): ◻

------

Furnished as Exhibit 99.1 to this Report on Form 6-K are the unaudited financial statements of ProQR Therapeutics N.V. (the "Company") for the three and nine-month periods ended September 30, 2025, and furnished as Exhibit 99.2 to this Report on Form 6-K is a press release of ProQR Therapeutics N.V. dated November 6, 2025, announcing the Company's results for the three and nine-month periods ended September 30, 2025.

On November 6, 2025, the Company issued a press release titled, "ProQR Announces Third Quarter 2025 Operating and Financial Results," announcing the Company's results for the three and nine-month periods ended September 30, 2025 and providing a business update. A copy of this press release is attached hereto as Exhibit 99.2 and is incorporated herein by reference.

ProQR hereby incorporates by reference the information contained herein into ProQR's registration statements on Form F-3 (File No. 333-282419, File No. 333-270943, File No. 333-263166 and File No. 333-285767).

------

**INDEX TO EXHIBITS**

---

| | |
|:---|:---|
| **Number** | **Description** |
| 99.1 | [Unaudited financial statements of ProQR Therapeutics N.V. for the three and nine-month periods ended September 30, 2025.](prqr-20250930xex99d1.htm) |
| 99.2 | [Press Release of ProQR Therapeutics N.V. dated November 6, 2025, announcing the Company's results for the three and nine-month periods ended September 30, 2025.](prqr-20250930xex99d2.htm) |

---

------

**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.

---

| | | |
|:---|:---|:---|
|  | **PROQR THERAPEUTICS N.V.** | **PROQR THERAPEUTICS N.V.** |
| Date: November 6, 2025 | By: | /s/ Dennis Hom |
|  |  | Dennis Hom |
|  |  | Chief Financial Officer |

---

------

## Exhibit 99.1

?xml version='1.0' encoding='ASCII'? ProQR Therapeutics N.V._2025-09-30

[**Table of Contents**](#TOC)

**Exhibit 99.1**

#### PROQR THERAPEUTICS N.V. Index to Unaudited Condensed Consolidated Financial Statements

---

| | |
|:---|:---|
|  | PAGE |
| [Unaudited Condensed Consolidated Statement of Financial Position at September 30, 2025 and December 31, 2024](#Statement_of_Financial_Position) | 1 |
| [Unaudited Condensed Consolidated Statement of Profit or Loss and Other Comprehensive Income for the Three and Nine Month Periods ended September 30, 2025 and 2024](#Statement_of_Profit_or_Loss_and_OCI) | 2 |
| [Unaudited Condensed Consolidated Statement of Changes in Equity for the Nine Month Periods Ended September 30, 2025 and 2024](#Statement_of_Changes_in_Equity) | 3 |
| [Unaudited Condensed Consolidated Statement of Cash Flows for the Three and Nine Month Periods ended September 30, 2025 and 2024](#Statement_of_Cash_Flows) | 4 |
| [Notes to Unaudited Condensed Consolidated Financial Statements](#NotestoUnauditedCondensedConsolidatedFin) | 5 |

---

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### PROQR THERAPEUTICS N.V. Unaudited Condensed Consolidated Statement of Financial Position

---

| | | | |
|:---|:---|:---|:---|
|  |  | **September 30,** <br>**2025** | **December 31,** <br>**2024** |
|  |  | *€1,000* | *€1,000* |
| **Assets** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Property, plant and equipment | 7 | 13018  | 14113  |
| &nbsp;&nbsp;&nbsp;&nbsp;Investments in financial assets | 17 | —  | —  |
| &nbsp;&nbsp;**Non-current assets** |  | **13018**  | **14113**  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash and cash equivalents | 5 | 106883  | 149408  |
| &nbsp;&nbsp;&nbsp;&nbsp;Prepayments and other receivables | 6 | 3872  | 3747  |
| &nbsp;&nbsp;&nbsp;&nbsp;Other taxes |  | 576  | 690  |
| &nbsp;&nbsp;**Current assets** |  | **111331**  | **153845**  |
| **Total assets** |  | **124349**  | **167958**  |
| **Equity and liabilities** |  |  |  |
| **Equity** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Equity attributable to owners of the Company |  | 57071  | 88560  |
| **Total equity** | **12** | **57071**  | **88560**  |
| **Liabilities** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Borrowings | 9 | —  | —  |
| &nbsp;&nbsp;&nbsp;&nbsp;Lease liabilities | 10 | 10017  | 11067  |
| &nbsp;&nbsp;&nbsp;&nbsp;Deferred income | 11 | 24125  | 29429  |
| &nbsp;&nbsp;**Non-current liabilities** |  | **34142**  | **40496**  |
| &nbsp;&nbsp;&nbsp;&nbsp;Borrowings | 9 | 4800  | 4582  |
| &nbsp;&nbsp;&nbsp;&nbsp;Lease liabilities | 10 | 1674  | 1567  |
| &nbsp;&nbsp;&nbsp;&nbsp;Derivative financial instruments | 9 | 292  | 468  |
| &nbsp;&nbsp;&nbsp;&nbsp;Trade payables |  | 305  | 16  |
| &nbsp;&nbsp;&nbsp;&nbsp;Social securities and other taxes |  | 121  | 1478  |
| &nbsp;&nbsp;&nbsp;&nbsp;Deferred income | 11 | 17394  | 21942  |
| &nbsp;&nbsp;&nbsp;&nbsp;Other current liabilities | 8 | 8550  | 8849  |
| &nbsp;&nbsp;**Current liabilities** |  | **33136**  | **38902**  |
| **Total liabilities** |  | **67278**  | **79398**  |
| **Total equity and liabilities** |  | **124349**  | **167958**  |

---

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### PROQR THERAPEUTICS N.V. Unaudited Condensed Consolidated Statement of Profit or Loss and Other Comprehensive Income
(€ in thousands, except share and per share data)

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
|  |  | **Three month period** | **Three month period** | **Nine month period** | **Nine month period** |
|  |  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  |
|  |  | **2025** | **2024** | **2025** | **2024** |
|  |  | *€1,000* | *€1,000* | *€1,000* | *€1,000* |
| **Revenue** | **13** | **2882**  | **3843**  | **11218**  | **14598**  |
| **Other income** | **14** | **33**  | **138**  | **413**  | **504**  |
| Research and development costs | 15 | (11080) | (9414) | (34811) | (25745) |
| General and administrative costs | 16 | (3119) | (3283) | (11169) | (9748) |
| **Total operating costs** |  | **(14199)** | **(12697)** | **(45980)** | **(35493)** |
| **Operating result** |  | **(11284)** | **(8716)** | **(34349)** | **(20391)** |
| Finance income and expense |  | 280  | 469  | 927  | 1470  |
| Results related to financial liabilities measured at fair value through profit or loss |  | (2) | 139  | 176  | 266  |
| **Result before corporate income taxes** |  | **(11006)** | **(8108)** | **(33246)** | **(18655)** |
| Income taxes | 18 | —  | —  | (18) | 197  |
| **Result for the period** |  | **(11006)** | **(8108)** | **(33264)** | **(18458)** |
| Other comprehensive income (foreign exchange differences on foreign operation) |  | (23) | (377) | (1076) | (101) |
| **Total comprehensive income**  |  | **(11029)** | **(8485)** | **(34340)** | **(18559)** |
| **Result attributable to** |  |  |  |  |  |
| Owners of the Company |  | (11006) | (8108) | (33264) | (18458) |
| Non-controlling interests |  | —  | —  | —  | —  |
|  |  | **(11006)** | **(8108)** | **(33264)** | **(18458)** |
| **Total comprehensive income attributable to** |  |  |  |  |  |
| Owners of the Company |  | (11029) | (8485) | (34340) | (18559) |
| Non-controlling interests |  | —  | —  | —  | —  |
|  |  | **(11029)** | **(8485)** | **(34340)** | **(18559)** |
| **Share information** |  |  |  |  |  |
| Weighted average number of shares outstanding<sup>1</sup> |  | 105344996  | 81682296  | 105328752  | 81639533  |
| **Earnings per share attributable to owners of the Company (Euro per share)** |  |  |  |  |  |
| Basic loss per share<sup>1</sup> |  | (0.10) | (0.10) | (0.32) | (0.23) |
| Diluted loss per share<sup>1</sup> |  | (0.10) | (0.10) | (0.32) | (0.23) |

---

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

&nbsp;&nbsp;&nbsp;&nbsp;1. For these periods the potential exercise of share options is not included in the diluted earnings per share as the Company was loss-making. Due to the anti-dilutive nature of the outstanding options, basic and diluted earnings per share are equal .

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### PROQR THERAPEUTICS N.V. Unaudited Condensed Consolidated Statement of Changes in Equity

---

| | | | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|:---|:---|
|  |  | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** |
|  |  | **Numberof shares** | **ShareCapital** | **SharePremium** | **Equity settledEmployeeBenefitReserve** | **TranslationReserve** | **AccumulatedDeficit** | **TotalEquity** |
|  |  |  | *€1,000* | *€1,000* | *€1,000* | *€1,000* | *€1,000* | *€1,000* |
| **Balance at January 1, 2024** |  | **84248384**  | **3370**  | **412894**  | **25159**  | **817**  | **(400850)** | **41390**  |
| Result for the period |  | —  | —  | —  | —  | —  | (18458) | **(18458)** |
| Other comprehensive income |  | —  | —  | —  | —  | (101) | —  | **(101)** |
| Recognition of share-based payments |  | —  | —  | —  | 1976  | —  | —  | **1976**  |
| Treasury shares transferred |  | (329675) | —  | —  | —  | —  | —  | **—**  |
| Share options lapsed |  | —  | —  | —  | (994) | —  | 994  | **—**  |
| Share options exercised / RSUs vested |  | 328597  | —  | 175  | (291) | —  | 291  | **175**  |
| **Balance at September 30, 2024** |  | **84247306**  | **3370**  | **413069**  | **25850**  | **716**  | **(418023)** | **24982**  |
| **Balance at January 1, 2025** |  | **107710916**  | **4308**  | **483812**  | **26248**  | **1350**  | **(427158)** | **88560**  |
| Result for the period |  | —  | —  | —  | —  | —  | (33264) | (33264) |
| Other comprehensive income |  | —  | —  | —  | —  | (1076) | —  | (1076) |
| Recognition of share-based payments |  | —  | —  | —  | 2784  | —  | —  | 2784  |
| Treasury shares transferred |  | (132665) | —  | —  | —  | —  | —  | —  |
| Share options lapsed |  | —  | —  | —  | (1532) | —  | 1532  | —  |
| Share options exercised / RSUs vested |  | 132665  | —  | 67  | (184) | —  | 184  | 67  |
| **Balance at September 30, 2025** |  | **107710916**  | **4308**  | **483879**  | **27316**  | **274**  | **(458706)** | **57071**  |

---

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### PROQR THERAPEUTICS N.V. Unaudited Condensed Consolidated Statement of Cash Flows

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
|  |  | **Three month period**  | **Three month period**  | **Nine month period**  | **Nine month period**  |
|  |  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  |
|  |  | **2025** | **2024** | **2025** | **2024** |
|  |  | €1*,000* | €1*,000* | €1*,000* | €1*,000* |
| **Cash flows from operating activities** |  |  |  |  |  |
| Net result |  | (11006) | (8108) | (33264) | (18458) |
| Adjustments for: |  |  |  |  |  |
| — Other income | 14 | (33) | —  | (413) | —  |
| — Depreciation |  | 671  | 688  | 2024  | 2090  |
| — Share-based compensation | 12 | 1117  | 612  | 2784  | 1976  |
| — Financial income and expenses |  | (280) | (469) | (927) | (1470) |
| — Results related to financial liabilities measured at fair value through profit or loss |  | 2  | (139) | (176) | (266) |
| — Income tax expenses | 18 | —  | —  | 18  | (197) |
| Changes in working capital |  | (3074) | 1117  | (10974) | (12721) |
| *Cash used in operations* |  | *(12603)* | *(6299)* | *(40928)* | *(29046)* |
| Corporate income tax received / (paid) |  | —  | 1  | (18) | 197  |
| Interest received |  | 519  | 860  | 1924  | 2402  |
| Interest paid |  | (151) | (219) | (412) | (598) |
| ***Net cash used in operating activities*** |  | ***(12235)*** | ***(5657)*** | ***(39434)*** | ***(27045)*** |
| **Cash flow from investing activities** |  |  |  |  |  |
| Increase in financial asset - current |  | —  | —  | —  | (17000) |
| Decrease in financial asset - current |  | —  | 17000  | —  | 17000  |
| Purchases of property, plant and equipment |  | (169) | (286) | (494) | (1285) |
| ***Net cash (used in) / generated by investing activities*** |  | ***(169)*** | ***16714***  | ***(494)*** | ***(1285)*** |
| **Cash flow from financing activities** |  |  |  |  |  |
| Proceeds from exercise of share options | 12 | —  | 1  | 67  | 175  |
| Repayment of lease liability | 10 | (444) | (454) | (1304) | (1329) |
| ***Net cash used in financing activities*** |  | ***(444)*** | ***(453)*** | ***(1237)*** | ***(1154)*** |
| **Net (decrease) / increase in cash and cash equivalents** |  | **(12848)** | **10604**  | **(41165)** | **(29484)** |
| Currency effect cash and cash equivalents |  | (34) | (173) | (1360) | (40) |
| Cash and cash equivalents, at beginning of the period | 5 | 119765  | 78970  | 149408  | 118925  |
| **Cash and cash equivalents at the end of the period** |  | **106883**  | **89401**  | **106883**  | **89401**  |

---

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### PROQR THERAPEUTICS N.V. Notes to Unaudited Condensed Consolidated Financial Statements
**1. General Information**

ProQR Therapeutics N.V., or "ProQR" or the "Company", is a biotechnology company domiciled in the Netherlands that primarily focuses on the discovery and development of novel therapeutic medicines.

Since September 18, 2014, the Company's ordinary shares have been listed on Nasdaq. They are currently trading at Nasdaq Capital Market under ticker symbol PRQR.

The Company was incorporated in the Netherlands, on February 21, 2012 (Chamber of Commerce no. 54600790) and was reorganized from a private company with limited liability to a public company with limited liability on September 23, 2014. The Company has its statutory seat in Leiden, the Netherlands. The address of its headquarters and registered office is Zernikedreef 9, 2333 CK Leiden, the Netherlands.

ProQR Therapeutics N.V. is the ultimate parent company of the following entities:

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics Holding B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics I B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics II B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics III B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics IV B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics V B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics VI B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics VII B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics VIII B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics IX B.V. (100%);

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR Therapeutics I Inc. (100%)

ProQR Therapeutics N.V. is also statutory director of Stichting Bewaarneming Aandelen ProQR ("ESOP Foundation") and has full control over this entity.

As used in these condensed consolidated financial statements, unless the context indicates otherwise, all references to "ProQR" or the "Company" refer to ProQR Therapeutics N.V. including its subsidiaries and the ESOP Foundation.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

**2. Significant Accounting Policies**

These interim condensed consolidated financial statements for the three and nine month periods ended September 30, 2025, have been prepared in accordance with IAS 34 Interim Financial Statements. They should be read in conjunction with the Company's annual financial statements for the year ended December 31, 2024. These interim condensed consolidated financial statements do not include all information required for a complete set of financial statements prepared in accordance with IFRS Standards. However, selected explanatory notes are included to explain events and transactions that are significant to an understanding of the changes in the Company's financial position and performance since the last annual financial statements. In the opinion of management, all events and transactions that are significant to an understanding of the changes in financial position and performance of the Company since the end of the last annual reporting period are disclosed in these interim condensed consolidated financial statements. The accounting policies adopted in the preparation of the interim condensed consolidated financial statements are consistent with those applied in the preparation of the Company's annual financial statements for the year ended December 31, 2024.

During the nine month period ended September 30, 2024, the Company invested in financial assets in the form of a deposit with an original maturity of longer than three months but shorter than twelve months which are measured at amortized cost as they give rise on specified dates to cash flows that are solely payments of principal and interest on the principal amount outstanding. The deposit matured on September 30, 2024.

The Company's financial results have varied substantially, and are expected to continue to vary, from period to period. The Company believes that its ordinary activities are not linked to any particular seasonal factors.

The management of ProQR has, upon preparing and finalizing these interim condensed consolidated financial statements, assessed the Company's ability to fund its operations for a period of at least one year after the date of signing these interim condensed consolidated financial statements. Management expects the Company to continue as a going concern based on its existing funding, taking into account the Company's current cash position and the projected cash flows based on the activities under execution on the basis of ProQR's business plan and budget. Thus, we continue to adopt the going concern basis of accounting in preparing the interim condensed consolidated financial statements.

The carrying amount of all financial assets and financial liabilities is a reasonable approximation of the fair value and therefore, information about the fair values of each class has not been disclosed.

The Company operates in one reportable segment, which comprises the discovery and development of innovative, RNA based therapeutics.

**3. Adoption of New and Revised International Financial Reporting Standards**

New Standards and Interpretations, which became effective as of January 1, 2025, did not have a material impact on our condensed consolidated financial statements.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

**4. Critical Accounting Estimates and Judgements**

In the application of the Company's accounting policies, management is required to make judgments, estimates and assumptions about the carrying amounts of assets and liabilities that are not readily apparent from other sources. The estimates and associated assumptions are based on historical experience and other factors that are considered to be relevant. Actual results may differ from these estimates.

The estimates and underlying assumptions are reviewed on an ongoing basis. Revisions to accounting estimates are recognized in the period in which the estimate is revised if the revision affects only that period or in the period of the revision and future periods if the revision affects both current and future periods.

The significant judgements made by management in applying the Company's accounting policies and the key sources of estimation uncertainty were the same as those described in the Company's annual financial statements for the year ended December 31, 2024.

*(i) Revenue recognition for the Eli Lilly and Company research and collaboration agreement*

a. Identification of the performance obligations

As further described in Note 13 the identification of the performance obligations for the Company's original research and collaboration agreement with Eli Lilly and Company ("Lilly"), and the amended and restated research and collaboration agreement (collectively, the "Collaboration agreement") involves significant judgement.

A key judgement was made in determining that the license granted to Lilly is not distinct from the associated research and development ("R&D") services, due to the lack of stand-alone value of the license without the Company's involvement and the significant interdependencies between the license and the R&D services to be provided by the Company. As a result, the license and the R&D services are accounted for together as a single combined performance obligation consisting of multiple activities that are not distinct.

b. Determining the timing of satisfaction of performance obligations

As further described in Note 13, before the handover of a compound to Lilly, the Company recognizes revenue over time, using an input method that estimates the satisfaction of the performance obligation as the percentage of labor hours incurred compared to the total estimated labor hours required to complete the promised services. As the Company's estimate of the total labor hours required is dependent on the evolution of the research and development activities, it may be subject to change. If the progression and/or outcome of certain research and development activities would be different from the assumptions that were made during the preparation of these financial statements, this could lead to material adjustments to the total estimated labor hours, which might result in a reallocation of revenue between current and future periods. Our total deferred revenue balance related to this Lilly performance obligation amounts to € 41,492,000 at September 30, 2025 (December 31, 2024: € 50,930,000).

c. Determining the transaction price

The Company applied judgement to determine whether the equity investments made by Lilly in ProQR are part of the transaction price for the Collaboration agreement. The Company concluded that the differences between the prices that Lilly paid for the shares and the ProQR stock closing prices on the days of entering into the equity investment agreements arose because of the Company's existing obligations to deliver research and development services to Lilly under the terms of the Collaboration agreement. Therefore, the above differences between the closing share prices on the agreement effective dates and the equity investment prices paid by Lilly are considered to be part of the transaction price of the contract and are initially allocated to deferred revenue.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

The contract also includes variable consideration, but no variable consideration was included in the initial transaction price at the inception, as it was not highly probable that a significant reversal in the amount of cumulative revenue recognized would not occur. The Company includes such variable consideration in the transaction price when the uncertainty associated with the variable consideration is resolved.

The Collaboration agreement includes variable consideration in the form of development milestones, commercial milestones, and sales-based royalties based on the level of sales. As further described in Note 13, during 2025, the Company achieved development milestones during the ProQR research program under the agreement, which were added to the transaction price and recognized partially as revenue during 2025 based on the status of completion (satisfied part) of the single combined performance obligation.

*(ii) Research and development expenditures*

Research expenditures are reflected in the income statement. Development expenses are currently also reflected in the income statement because the criteria for capitalization are not met. At each balance sheet date, the Company estimates the level of service performed by the vendors and the associated costs incurred for the services performed.

Although we do not expect the estimates to be materially different from amounts actually incurred, the understanding of the status and timing of services performed relative to the actual status and timing of services performed may vary and could result in reporting amounts that are too high or too low in any particular period.

**5. Cash and Cash Equivalents**

At September 30, 2025, the Company's cash and cash equivalents were € 106,883,000 compared to € 149,408,000 at December 31, 2024. The cash balances are held at banks with investment grade credit ratings. Short-term credit ratings must be rated A-1/P-1/F1 at a minimum by at least one of the Nationally Recognized Statistical Rating Organizations ("NRSROs") specifically Moody's, Standard & Poor's or Fitch. The cash at banks is at full disposal of the Company. Included in cash and cash equivalents are deposits fixed for at most 3-month periods at a time.

**6. Prepayments and Other Receivables**

---

| | | |
|:---|:---|:---|
|  | **September 30,**<br>**2025** | **December 31,**<br>**2024** |
|  | €1*,000* | €1*,000* |
| Prepayments | 1903 | 2410  |
| Other receivables | 1467 | 835  |
| Accrued income from Rett Syndrome Research Trust | 502 | 502  |
|  | **3872**  | **3747**  |

---

All receivables are considered short-term and due within one year. At September 30, 2025 and December 31, 2024 prepayments consisted principally of payments made by the Company for services not yet provided by vendors. At September 30, 2025 other receivables consisted principally of amounts receivable from research collaboration partners, accrued income and deposits. At December 31, 2024 other receivables consisted principally of accrued grant income and deposits. As at September 30, 2025 and December 31, 2024 the accrued grant income relating to Rett Syndrome Research Trust ("RSRT") includes the initial fair value of the warrants issued to RSRT that was accounted for as a reduction of the transaction price. The RSRT agreement is described in Note 14. Other Income.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

**7. Property, Plant and Equipment**

At September 30, 2025, and December 31, 2024, property plant and equipment consisted of buildings and leasehold improvements, laboratory equipment and other assets. Buildings and leasehold improvements include a right-of-use asset relating to the lease of our Leiden office and laboratory space, with a carrying amount of € 10,448,000 at September 30, 2025 (December 31, 2024: € 11,433,000).

**8. Other Current Liabilities**

At September 30, 2025, other current liabilities amount to € 8,550,000 (December 31, 2024: € 8,849,000). At September 30, 2025 and December 31, 2024, other current liabilities consisted principally of accruals for services provided by vendors not yet billed, payroll related accruals and other miscellaneous liabilities.

#### 9 . Borrowings

---

| | | |
|:---|:---|:---|
|  | **September 30,** <br>**2025** | **December 31,**<br>**2024** |
|  | *€1,000* | *€1,000* |
| Innovation credit | 2899  | 2899  |
| Accrued interest on innovation credit | 1901  | 1683  |
| **Total borrowings** | **4800**  | **4582**  |
| Current portion | 4800  | 4582  |
| **Total non-current borrowings** | **—**  | **—**  |

---

In December 2018, ProQR was awarded an Innovation credit for the sepofarsen program. Amounts were drawn under this facility from 2018 through 2022. The credit of € 3,907,000 was used to conduct the Phase 2/3 clinical study and efforts to obtain regulatory and ethical market approval (New Drug Applications ("NDA") / Marketing Authorization Applications ("MAA")) of sepofarsen for LCA10. In the fourth quarter of 2023, ProQR made a partial repayment of the principal, amounting to € 1,008,000. The remaining amount payable of € 2,899,000 is recognized under current borrowings as at September 30, 2025 and December 31, 2024.

In December 2023, ProQR received a waiver for the remaining balance of the Innovation credit including accrued interest. As a result, the repayment of the total loan of € 4,292,000, including accrued interest, could be waived if conditions are met, subject to annual review. In January 2025, the waiver for the principal and interest was again extended until December 31, 2025.

In September 2022, ProQR extinguished its debt with Pontifax and Kreos by repaying all outstanding principal amounts. However, the Pontifax' and Kreos' warrants, classified as derivative financial instruments on the balance sheet, remain in place until their five-year economic life expires in 2025 and 2026. These warrants are accounted for as embedded derivatives and were recognized separately from the host contract as derivative financial liabilities at fair value through profit or loss. During Q3 2025, the original Pontifax warrants expiring in July 2025 and the Kreos warrants expiring in August 2025 expired and were derecognized.

**10. Lease Liabilities**

At September 30, 2025 and December 31, 2024, lease liabilities primarily consisted of the Company's lease of office and laboratory facilities at Zernikedreef in Leiden, the Netherlands.

The Company leases office and laboratory facilities of 4,818 square meters at Zernikedreef in Leiden, the Netherlands, where our headquarters and our laboratories are located. The current lease agreement for these facilities terminates

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

on June 30, 2031. The lease agreement contains no significant dismantling requirements.

The initial 10-year lease agreement for the Leiden office and laboratory facilities was accounted for as of commencement date July 1, 2020. This 10-year period was extended by 1 year to an 11-year period in December 2020. The lease contract may be extended for subsequent 5-year periods. As the Company is not reasonably certain to exercise these extension options, these are not included in the lease term.

The carrying amount of the right-of-use asset is disclosed in Note 7.

**11. Deferred Income**

The following table summarizes details of deferred income at September 30, 2025 and December 31, 2024. The nature of the deferred income is described in Note 13 and 14.

---

| | | |
|:---|:---|:---|
|  | **September 30,** <br>**2025** | **December 31,** <br>**2024** |
|  | €1*,000* | €1*,000* |
| Payments from Eli Lilly and Company | 17367  | 21501  |
| Payments from Rett Syndrome Research Trust | 27  | 441  |
| **Current deferred income** | **17394**  | **21942**  |
| Payments from Eli Lilly and Company | 24125  | 29429  |
| **Non-current deferred income** | **24125**  | **29429**  |
| **Total deferred income** | **41519**  | **51371**  |

---

c

**12. Shareholders' Equity**

The authorized share capital of the Company amounting to € 13,600,000 consists of 170,000,000 ordinary shares and 170,000,000 preference shares with a par value of € 0.04 per share. At September 30, 2025, 107,710,916 ordinary shares were issued, 105,345,192 ordinary shares were fully paid and 2,365,724 ordinary shares were held by the Company as treasury shares (December 31, 2024: 2,498,389).

In September 2024, the Company filed a shelf registration statement on Form F-3, which permitted: (a) the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $300,000,000 of its ordinary shares, warrants and/or units; and (b) as part of the $300,000,000, the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $75,000,000 of its ordinary shares that may be issued and sold under a sales agreement (the "sales agreement") with Cantor Fitzgerald & Co. ("Cantor") in one or more at-the-market ("ATM") offerings. The Company will pay Cantor a commission equal to 3% of the gross proceeds of the sales price of all ordinary shares sold through it as sales agent under the sale agreement. As of September 30, 2025, no shares have been issued pursuant to this ATM facility.

In October 2024, the Company consummated an underwritten public offering of 18,000,000 ordinary shares (the "offering") at a public offering price of $3.50 per share (the "public offering price"). In addition, the Company granted the underwriters a 30-day option to purchase up to 2,700,000 additional ordinary shares at the public offering price, less underwriting discounts and commissions. The option was partially exercised on October 31, 2024, resulting in the issuance of 1,940,072 shares. The gross proceeds from the Offering and subsequent partial exercise of the underwriters' option, amounted to $69,790,000 (€ 64,600,000) while the transaction costs amounted to approximately € 4,365,000, resulting in net proceeds of approximately € 60,235,000.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

Concurrently with the Offering, the Company entered into a share purchase agreement with Lilly in a separately negotiated transaction (the "concurrent private placement"), pursuant to which the Company agreed to offer and sell, and Lilly agreed to purchase, 3,523,538 ordinary shares at a price per share equal to the public offering price, for total gross proceeds of approximately $12,300,000, subject to a purchase price cap of $15,000,000, the consummation of the Offering and the satisfaction of other customary closing conditions. The proceeds of $12,300,000 (€ 11,400,000) from the concurrent private placement were received on October 25, 2024. The ordinary shares purchased in the concurrent private placement are not subject to any underwriting discounts or commissions.

*Translation reserve*

The translation reserve comprises all foreign currency differences arising from the translation of the financial statements of foreign operations.

*Share options*

The Company operates an equity-settled share-based compensation plan, which was introduced in 2013. Options and Restricted Stock Units ("RSUs") may be granted to employees, members of the Board and consultants. The compensation expenses included in operating costs for this plan in the nine month period ended September 30, 2025 were € 2,784,000 (nine month period ended September 30, 2024: € 1,976,000), of which € 1,952,000 was recorded in general and administrative costs (nine month period ended September 30, 2024: € 1,559,000) and € 832,000 was recorded in research and development costs (nine month period ended September 30, 2024: € 417,000).

**13. Revenue**

*Eli Lilly and Company collaboration*

In September 2021, the Company entered into a global licensing and research collaboration with Lilly focused on the discovery, development, and commercialization of potential new medicines for genetic disorders in the liver and nervous system. ProQR and Lilly will use ProQR's proprietary Axiomer™ RNA editing platform to progress new drug targets toward clinical development and commercialization.

Under the terms of the agreement, ProQR received an upfront payment and equity consideration, and is eligible to receive milestone payments and royalties on the net sales of any resulting products. In September 2021, the Company issued 3,989,976 shares to Lilly, resulting in gross proceeds of $30,000,000 (€ 25,270,000). These shares were issued at a premium of $2,429,000 (€ 2,047,000), which was determined to be part of the transaction price and as such was initially recognized as deferred revenue. An up-front payment of $20,000,000 (€ 16,849,000) was received in October 2021.

In December 2022, the Company and Lilly amended their research and collaboration agreement described above, which expanded the collaboration. Under the amended and restated research and collaboration agreement, Lilly will gain access to additional targets in the central nervous system ("CNS") and peripheral nervous system ("PNS") with ProQR's Axiomer platform.

As described under Note 12, pursuant to the amended and restated agreement, the Company issued 9,381,586 shares to Lilly in December 2022, resulting in gross proceeds of $15,000,000 (€ 14,122,000). These shares were issued at a discount of $480,000 (€ 451,000), which is accounted for as a reduction of the transaction price. In February 2023, ProQR also received an upfront payment of $60,000,000 (€ 56,412,000). Lilly has the ability to exercise an option to further expand the partnership for a consideration of $50,000,000.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

With regard to the original and amended and restated research and collaboration agreements with Lilly, the Company concluded as follows:

● The amended and restated research and collaboration agreement is accounted for as a separate contract under IFRS 15 given the group of promises to be delivered are distinct and are priced commensurate with stand-alone selling prices.

● For each of the agreements, the company identified one performance obligation under IFRS 15, for the transfer of a license combined with the performance of research and development activities. The Company concluded that the license is not capable of being distinct and is not distinct in the context of the contract. ProQR's services are evaluated as predominant at inception of the contract and the compounds resulting from the collaboration do not represent a series of distinct promises because they were not predetermined at the inception of the contract and can be terminated or replaced at the discretion of Lilly subject to the terms and conditions of the Collaboration agreement.

● The transaction price of the agreement includes fixed components, consisting of an up-front fee and an equity component (premium or discount). The agreement also contains variable parts, notably milestones, which are included in the transaction price to the extent that it is highly probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Development milestone payments to be reached during the ProQR research program will only be included to the extent that it is highly probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the milestones is subsequently resolved. Sales-based milestones and sales-based royalties will be included as the underlying sales occur.

● Initially, the Company recognizes revenue over time, using an input method that estimates the satisfaction of the performance obligation as the percentage of labor hours incurred compared to the total estimated labor hours required to complete the promised services.

After the handover of a compound to Lilly:

● The variable consideration for development milestones to be reached during the Lilly R&D activities is linked to a separable right to use the license which comes into existence for each successful compound transferred to Lilly. This license is a separate performance obligation and revenue will be recognized at a point in time when the development milestone for a license is achieved and the variable constraint is resolved.

● The variable consideration for commercial milestones is linked to a separable right to use the license which comes into existence for each successful compound transferred to Lilly. This license is a separate performance obligation and will be recognized at a point in time when the commercial milestone for a license is achieved and the variable constraint is resolved.

● For sales-based royalties, the license is the predominant item to which the royalty relates. The sales-based royalties will be recognized after the handover of the compound to Lilly (after completion of the initial performance obligation) and once the respective sale level occurs.

During the nine month period ended September 30, 2025, the Company reached milestones amounting to $2,000,000 (€ 1,781,000) under the agreement, which was added to the transaction price and recognized partially as revenue during the nine month period ended September 30, 2025.

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

**14. Other Income**

---

| | | |
|:---|:---|:---|
|  | **Nine month period**  | **Nine month period**  |
|  | **ended September 30,**  | **ended September 30,**  |
|  | **2025** | **2024** |
|  | *€1,000* | *€1,000* |
| Grant income | 413  | 504  |
|  | **413**  | **504**  |

---

In January, 2024, the Company entered into an agreement with the RSRT that focuses on the design and development of editing oligonucleotides ("EONs") using the Company's Axiomer technology platform targeting the transcription factor Methyl CpG binding protein 2 ("MECP2") and correcting mutations of interest. Under the agreement, RSRT awarded the Company up to € 1,015,000 as a research grant for the initial phase of the project that was received during 2024. Of this grant € 504,000 was recognized as Other Income during the nine month period ended September 30, 2024, and € 413,000 recognized as Other Income for the nine month period ended September 30, 2025. The balance was recorded as Deferred Income in 2024 and 2025.

In December 2024, the Company expanded partnership with RSRT to include an additional $8,150,000 in funding from the RSRT to support the advancement of the selected candidates into clinical trials. As at September 30, 2025 no amounts have been received under this agreement and the work has not yet commenced.

Grants are recognized in other income in the same period in which the related R&D costs are recognized.

**15. Research and Development Costs**

Research and development costs amount to € 34,811,000 for the nine month period ended September 30, 2025 (nine month period ended September 30, 2024: € 25,745,000) and are comprised of allocated employee costs including share-based payments, the costs of materials and laboratory consumables, outsourced activities, license and intellectual property costs and other allocated costs. Research and development costs increased compared to the same period in the prior year, mainly due to the Company's increased outsourced research and development activities in the nine month period of 2025 and increased full time employee equivalents ("FTE").

**16. General and Administrative Costs**

General and administrative costs amount to € 11,169,000 for the nine month period ended September 30, 2025 (nine month period ended September 30, 2024: € 9,748,000).

**17. Investments in Financial Assets**

Investment in financial assets consist of the Company's investment in Phoenicis Therapeutics Inc. ("Phoenicis") and Yarrow Biotechnology Inc. ("Yarrow").

ProQR holds a 3.9% interest in Phoenicis. As at September 30, 2025, the investment amounts to € nil (December 31, 2024: € nil). Phoenicis discontinued its research and development operational activities during the quarter ended September 30, 2024.

ProQR holds a 5.1% interest in Yarrow. As at September 30, 2025, the fair value of the Yarrow financial asset amounted to € nil (December 31, 2024: € nil).

[**Table of Contents**](#TOC)

Unaudited Condensed Consolidated Financial Statements

#### 18 . Income Taxes
The current income tax liability amounts to € nil at September 30, 2025 (December 31, 2024: € nil). No significant temporary differences exist between accounting and tax results. Realization of deferred tax assets is dependent on future earnings, if any, the timing and amount of which are uncertain. Accordingly, the Company has not yet recognized any deferred tax asset related to operating losses.

Tax losses in the Netherlands may be carried forward indefinitely. However, the offset of losses will be limited in a given year against the first € 1 million of taxable profit. For taxable profit in excess of this amount, losses may only be offset up to 50% of this excess. In addition, unused non-deductible interest expenses may be carried forward indefinitely. However, the offset will be limited in a given year against the higher of 20% of adjusted taxable profit or € 1.0 million of interest income.

**19. Related-Party Transactions**

The Company does not have any transactions with related parties other than compensation to its Board members.

**20. Events After Balance Sheet Date**

None.

## Exhibit 99.2

**Exhibit 99.2**

## ProQR Announces Third Quarter 2025 Operating and Financial Results
&nbsp;&nbsp;&nbsp;&nbsp;● Received CTA authorization for Phase 1 trial of lead program AX-0810, targeting NTCP for cholestatic diseases

&nbsp;&nbsp;&nbsp;&nbsp;● Initiating Phase 1 study of AX-0810 in healthy volunteers, with initial safety, tolerability, and PK data from Cohort 1 expected by year-end, and target engagement data from all cohorts in H1 2026

&nbsp;&nbsp;&nbsp;&nbsp;● € 106.9 million cash and cash equivalents as of end Q3 – providing runway into mid-2027

LEIDEN, Netherlands & CAMBRIDGE, Mass., November 6, 2025 – ProQR Therapeutics N.V. (Nasdaq: PRQR) (ProQR), a company dedicated to changing lives through transformative RNA therapies based on its proprietary Axiomer™ RNA editing technology platform, today reported its financial and operating results for the third quarter ended September 30, 2025, and provided a business update.

"Last month we achieved an important milestone with the CTA authorization and are initiating our first-in-human study for AX-0810, marking a significant step forward for both this program and our Axiomer RNA editing platform," said Daniel A. de Boer, Founder and Chief Executive Officer of ProQR. "This study represents the first clinical evaluation of an Axiomer editing oligonucleotide and positions us to deliver initial safety and PK data before year-end, followed by target engagement data in the first half of 2026. Supported by our strong cash position providing runway into mid-2027, we continue to advance our broader pipeline, platform, and partnership activities, executing on our strategy to deliver transformative RNA editing therapies for diseases with high unmet need."

#### Recent Progress and Anticipated Upcoming Events
&nbsp;&nbsp;&nbsp;&nbsp;● In November, the Company hosted a **virtual analyst and investor event focused on AX-0810**, highlighting the Phase 1 trial design and target engagement/biomarker strategy.

&nbsp;&nbsp;&nbsp;&nbsp;● **AX-0810** uses Axiomer's ability to modulate protein function by targeting NTCP for the treatment of cholestatic diseases. In October **AX-0810 received CTA authorization** and a first-in-human (FIH) Phase 1 study is being initiated in healthy volunteers. Initial safety, tolerability, and PK data for Cohort 1 is expected toward the end of 2025 with target engagement data for all healthy volunteer cohorts in the first half of 2026. In parallel,

------

activities are underway to include a patient cohort in this FIH following completion of the healthy volunteer cohorts.

&nbsp;&nbsp;&nbsp;&nbsp;● Beyond AX-0810, ProQR's Axiomer pipeline demonstrates the broad potential of RNA editing across three key applications – modulate, correct, and protect – with updates expected across these earlier-stage programs in the coming months.

● **AX-2402** applies Axiomer RNA editing to correct disease-causing mutations, targeting the R270X nonsense mutation in MECP2 to restore normal protein function for the treatment of Rett syndrome.

● **AX-2911** leverages Axiomer's ability to modulate protein activity by editing the I148M mutation in PNPLA3, the strongest known genetic risk factor for fatty liver disease.

● **AX-1412** demonstrates Axiomer's protective application, mimicking a naturally occurring B4GALT1 variant associated with significantly reduced cardiovascular risk.

&nbsp;&nbsp;&nbsp;&nbsp;● In October, the Company presented at the **Oligonucleotide Therapeutics Society (OTS) Annual Meeting** in Budapest, highlighting applications of its Axiomer RNA editing platform technology.

&nbsp;&nbsp;&nbsp;&nbsp;● ProQR continues to execute on partnership with Eli Lilly and Company (Lilly), with potential data updates and milestone income from the ongoing collaboration.

#### Financial Highlights
At September 30, 2025, ProQR held cash and cash equivalents of approximately € 106.9 million, compared to € 149.4 million at December 31, 2024.

Net cash used in operating activities during the nine-month period ended September 30, 2025 was € 39.4 million, compared to € 27.0 million used for the same period last year. During the first nine months of 2025, the Company achieved certain milestones in the collaboration agreement with Eli Lilly amounting to $2.0 million (~€ 1.8 million).

Research and development (R&D) costs were € 34.8 million for the nine month period ended September 30, 2025 compared to € 25.7 million for the same period last year.

General and administrative costs were € 11.2 million for the nine month period ended September 30, 2025 compared to € 9.7 million for the same period in 2024.

Net loss for the nine month period ended September 30, 2025 was € 33.3 million, or € 0.32 per diluted share, compared to € 18.5 million, or € 0.23 per diluted share, for the same period last year. For further financial information for the period ended September 30, 2025, please refer to the Q3 financial report 6-K filing.

------

#### About Axiomer™
ProQR is pioneering a next-generation RNA base editing technology called Axiomer™, which could potentially yield a new class of medicines for diverse types of diseases. Axiomer™ "Editing Oligonucleotides", or EONs, mediate single nucleotide changes to RNA in a highly specific and targeted way using molecular machinery that is present in human cells called ADAR (Adenosine Deaminase Acting on RNA). Axiomer™ EONs are designed to recruit and direct endogenously expressed ADARs to change an Adenosine (A) to an Inosine (I) in the RNA – an Inosine is translated as a Guanosine (G) – correcting an RNA with a disease-causing mutation back to a normal (wild type) RNA, modulating protein expression, or altering a protein so that it will have a new function that helps prevent or treat disease.

#### About ProQR
ProQR Therapeutics is dedicated to changing lives through the creation of transformative RNA therapies. ProQR is pioneering a next-generation RNA technology called Axiomer™, which uses a cell's own editing machinery called ADAR to make specific single nucleotide edits in RNA to reverse a mutation or modulate protein expression and could potentially yield a new class of medicines for both rare and prevalent diseases with unmet need. Based on our unique proprietary RNA repair platform technologies we are growing our pipeline with patients and loved ones in mind.

Learn more about ProQR at **www.proqr.com**.

#### 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 "continue," "anticipate," "believe," "could," "estimate," "expect," "goal," "intend," "look forward to", "may," "plan," "potential," "predict," "project," "should," "will," "would" and similar expressions. Such forward-looking statements include, but are not limited to, statements regarding our business, technology, strategy, preclinical and clinical model data, our initial pipeline targets and the upcoming strategic priorities and milestones related thereto, the continued advancement of our lead development pipeline programs, including ongoing and planned clinical trials, the planned Phase 1 clinical study of for AX-0810 in NTCP for cholestatic diseases, including the planned trial design, implementation and initiation in the Netherlands, and our ability to recruit for and complete a Phase 1 clinical trial for AX-0810 in healthy volunteers; expectations regarding the safety and therapeutic benefits of AX-0810, including the planned dosing levels and their efficacy; the anticipated timing of initial Phase 1 clinical data for our lead program, AX-0810, and other programs, the continued development and advancement of our Axiomer platform, the therapeutic potential of our Axiomer RNA editing oligonucleotides and product candidates, the timing, progress and results of our preclinical studies and other development and pipeline activities, including the release of data

------

related thereto, our patent estate, including our anticipated strength and our continued investment in it, as well as the timing of our clinical development, the potential of our technologies and product candidates, the collaboration with Lilly and the intended benefits thereof, including timing for data updates, potential milestones, exercise of an option to expand targets and the receipt of an opt-in payment, our ability to selectively form new partnerships and enter into future collaborations, and our financial position and cash-runway. 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. Our actual results could differ materially from those expressed or implied by these forward-looking statements for many reasons, including, without limitation, the risks, uncertainties and other factors in our filings made with the Securities and Exchange Commission, including certain sections of our most recent annual report filed on Form 20-F. These risks and uncertainties include, among others, the cost, timing and results of preclinical studies and clinical trials and other development activities by us and our collaborative partners whose operations and activities may be slowed or halted shortage and pressure on supply and logistics on the global market, economic sanctions and international tariffs; the likelihood of our preclinical and clinical programs being initiated and executed on timelines provided and reliance on our contract research organizations and predictability of timely enrollment of subjects and patients to advance our clinical trials and maintain their own operations; our reliance on contract manufacturers to supply materials for research and development and the risk of supply interruption from a contract manufacturer; the potential for future data to alter initial and preliminary results of early-stage clinical trials; the unpredictability of the duration and results of the regulatory review of applications or clearances that are necessary to initiate and continue to advance and progress our clinical programs; the ability to secure, maintain and realize the intended benefits of collaborations with partners, including the collaboration with Lilly; the possible impairment of, inability to obtain, and costs to obtain intellectual property rights; possible safety or efficacy concerns that could emerge as new data are generated in research and development; general business, operational, financial and accounting risks, and risks related to litigation and disputes with third parties; and risks related to macroeconomic conditions and market volatility resulting from global economic developments, geopolitical events and conflicts, high inflation, rising interest rates, tariffs and potential for significant changes in U.S. policies and regulatory environment. 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 and media contact:**<br>Sarah Kiely<br>ProQR Therapeutics N.V.<br>T: +1 617 599 6228<br>**skiely@proqr.com**<br>or

**Investor contact:**

Peter Kelleher<br>LifeSci Advisors<br>T: +1 617 430 7579<br>**pkelleher@lifesciadvisors.com**

------

#### Financial Tables

#### PROQR THERAPEUTICS N.V. <br> Unaudited Condensed Consolidated Statement of Financial Position

---

| | | |
|:---|:---|:---|
|  | **September 30,** <br>**2025** | **December 31,** <br>**2024** |
|  | €1*,000* | €1*,000* |
| **Assets** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Property, plant and equipment | 13018  | 14113  |
| &nbsp;&nbsp;&nbsp;&nbsp;Investments in financial assets | —  | —  |
| &nbsp;&nbsp;**Non-current assets** | **13018**  | **14113**  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash and cash equivalents | 106883  | 149408  |
| &nbsp;&nbsp;&nbsp;&nbsp;Prepayments and other receivables | 3872  | 3747  |
| &nbsp;&nbsp;&nbsp;&nbsp;Other taxes | 576  | 690  |
| &nbsp;&nbsp;**Current assets** | **111331**  | **153845**  |
| **Total assets** | **124349**  | **167958**  |
| **Equity and liabilities** |  |  |
| **Equity** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Equity attributable to owners of the Company | 57071  | 88560  |
| **Total equity** | **57071**  | **88560**  |
| **Liabilities** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Borrowings | —  | —  |
| &nbsp;&nbsp;&nbsp;&nbsp;Lease liabilities | 10017  | 11067  |
| &nbsp;&nbsp;&nbsp;&nbsp;Deferred income | 24125  | 29429  |
| &nbsp;&nbsp;**Non-current liabilities** | **34142**  | **40496**  |
| &nbsp;&nbsp;&nbsp;&nbsp;Borrowings | 4800  | 4582  |
| &nbsp;&nbsp;&nbsp;&nbsp;Lease liabilities | 1674  | 1567  |
| &nbsp;&nbsp;&nbsp;&nbsp;Derivative financial instruments | 292  | 468  |
| &nbsp;&nbsp;&nbsp;&nbsp;Trade payables | 305  | 16  |
| &nbsp;&nbsp;&nbsp;&nbsp;Social securities and other taxes | 121  | 1478  |
| &nbsp;&nbsp;&nbsp;&nbsp;Deferred income | 17394  | 21942  |
| &nbsp;&nbsp;&nbsp;&nbsp;Other current liabilities | 8550  | 8849  |
| &nbsp;&nbsp;**Current liabilities** | **33136**  | **38902**  |
| **Total liabilities** | **67278**  | **79398**  |
| **Total equity and liabilities** | **124349**  | **167958**  |

---

------

#### PROQR THERAPEUTICS N.V. <br> Unaudited Condensed Consolidated Statement of Profit or Loss and Other Comprehensive Income
(€ in thousands, except share and per share data)

---

| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three month period** | **Three month period** | **Nine month period** | **Nine month period** |
|  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  |
|  | **2025** | **2024** | **2025** | **2024** |
|  | €1*,000* | €1*,000* | €1*,000* | €1*,000* |
| **Revenue** | **2882**  | **3843**  | **11218**  | **14598**  |
| **Other income** | **33**  | **138**  | **413**  | **504**  |
| Research and development costs | (11080) | (9414) | (34811) | (25745) |
| General and administrative costs | (3119) | (3283) | (11169) | (9748) |
| **Total operating costs** | **(14199)** | **(12697)** | **(45980)** | **(35493)** |
| **Operating result** | **(11284)** | **(8716)** | **(34349)** | **(20391)** |
| Finance income and expense | 280  | 469  | 927  | 1470  |
| Results related to financial liabilities measured at fair value through profit or loss | (2) | 139  | 176  | 266  |
| **Result before corporate income taxes** | **(11006)** | **(8108)** | **(33246)** | **(18655)** |
| Income taxes | —  | —  | (18) | 197  |
| **Result for the period** | **(11006)** | **(8108)** | **(33264)** | **(18458)** |
| Other comprehensive income (foreign exchange differences on foreign operation) | (23) | (377) | (1076) | (101) |
| **Total comprehensive income**  | **(11029)** | **(8485)** | **(34340)** | **(18559)** |
| **Result attributable to** |  |  |  |  |
| Owners of the Company | (11006) | (8108) | (33264) | (18458) |
| Non-controlling interests | —  | —  | —  | —  |
|  | **(11006)** | **(8108)** | **(33264)** | **(18458)** |
| **Total comprehensive income attributable to** |  |  |  |  |
| Owners of the Company | (11029) | (8485) | (34340) | (18559) |
| Non-controlling interests | —  | —  | —  | —  |
|  | **(11029)** | **(8485)** | **(34340)** | **(18559)** |
| **Share information** |  |  |  |  |
| Weighted average number of shares outstanding<sup>1</sup> | 105344996  | 81682296  | 105328752  | 81639533  |
| **Earnings per share attributable to owners of the Company (Euro per share)** |  |  |  |  |
| Basic loss per share<sup>1</sup> | (0.10) | (0.10) | (0.32) | (0.23) |
| Diluted loss per share<sup>1</sup> | (0.10) | (0.10) | (0.32) | (0.23) |

---

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1. For these periods the potential exercise of share options is not included in the diluted earnings per share as the Company was loss-making. Due to the anti-dilutive nature of the outstanding options, basic and diluted earnings per share are equal.

------

#### PROQR THERAPEUTICS N.V. <br> Unaudited Condensed Consolidated Statement of Changes in Equity

---

| | | | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|:---|:---|
|  |  | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** | **Attributable to owners of the Company** |
|  |  | **Number<br>of shares** | **Share<br>Capital** | **Share<br>Premium** | **Equity settled<br>Employee<br>Benefit<br>Reserve** | **Translation<br>Reserve** | **Accumulated<br>Deficit** | **Total<br>Equity** |
|  |  |  | €1*,000* | €1*,000* | €1*,000* | €1*,000* | €1*,000* | €1*,000* |
| **Balance at January 1, 2024** |  | **84248384**  | **3370**  | **412894**  | **25159**  | **817**  | **(400850)** | **41390**  |
| Result for the period |  | —  | —  | —  | —  | —  | (18458) | **(18458)** |
| Other comprehensive income |  | —  | —  | —  | —  | (101) | —  | **(101)** |
| Recognition of share-based payments |  | —  | —  | —  | 1976  | —  | —  | **1976**  |
| Treasury shares transferred |  | (329675) | —  | —  | —  | —  | —  | **—**  |
| Share options lapsed |  | —  | —  | —  | (994) | —  | 994  | **—**  |
| Share options exercised / RSUs vested |  | 328597  | —  | 175  | (291) | —  | 291  | **175**  |
| **Balance at September 30, 2024** |  | **84247306**  | **3370**  | **413069**  | **25850**  | **716**  | **(418023)** | **24982**  |
| **Balance at January 1, 2025** |  | **107710916**  | **4308**  | **483812**  | **26248**  | **1350**  | **(427158)** | **88560**  |
| Result for the period |  | —  | —  | —  | —  | —  | (33264) | **(33264)** |
| Other comprehensive income |  | —  | —  | —  | —  | (1076) | —  | **(1076)** |
| Recognition of share-based payments |  | —  | —  | —  | 2784  | —  | —  | **2784**  |
| Treasury shares transferred |  | (132665) | —  | —  | —  | —  | —  | **—**  |
| Share options lapsed |  | —  | —  | —  | (1532) | —  | 1532  | **—**  |
| Share options exercised / RSUs vested |  | 132665  | —  | 67  | (184) | —  | 184  | **67**  |
| **Balance at September 30, 2025** |  | **107710916**  | **4308**  | **483879**  | **27316**  | **274**  | **(458706)** | **57071**  |

---

------

#### PROQR THERAPEUTICS N.V. <br> Unaudited Condensed Consolidated Statement of Cash Flows

---

| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three month period**  | **Three month period**  | **Nine month period**  | **Nine month period**  |
|  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  | **ended September 30,**  |
|  | **2025** | **2024** | **2025** | **2024** |
|  | €1*,000* | €1*,000* | €1*,000* | €1*,000* |
| **Cash flows from operating activities** |  |  |  |  |
| Net result | (11006) | (8108) | (33264) | (18458) |
| Adjustments for: |  |  |  |  |
| — Other income | (33) | —  | (413) | —  |
| — Depreciation | 671  | 688  | 2024  | 2090  |
| — Share-based compensation | 1117  | 612  | 2784  | 1976  |
| — Financial income and expenses | (280) | (469) | (927) | (1470) |
| — Results related to financial liabilities measured at fair value through profit or loss | 2  | (139) | (176) | (266) |
| — Income tax expenses | —  | —  | 18  | (197) |
| Changes in working capital | (3074) | 1117  | (10974) | (12721) |
| *Cash used in operations* | *(12603)* | *(6299)* | *(40928)* | *(29046)* |
| Corporate income tax received / (paid) | —  | 1  | (18) | 197  |
| Interest received | 519  | 860  | 1924  | 2402  |
| Interest paid | (151) | (219) | (412) | (598) |
| ***Net cash used in operating activities*** | ***(12235)*** | ***(5657)*** | ***(39434)*** | ***(27045)*** |
| **Cash flow from investing activities** |  |  |  |  |
| Increase in financial asset - current | —  | —  | —  | (17000) |
| Decrease in financial asset - current | —  | 17000  | —  | 17000  |
| Purchases of property, plant and equipment | (169) | (286) | (494) | (1285) |
| ***Net cash (used in) / generated by investing activities*** | ***(169)*** | ***16714***  | ***(494)*** | ***(1285)*** |
| **Cash flow from financing activities** |  |  |  |  |
| Proceeds from exercise of share options | —  | 1  | 67  | 175  |
| Repayment of lease liability | (444) | (454) | (1304) | (1329) |
| ***Net cash used in financing activities*** | ***(444)*** | ***(453)*** | ***(1237)*** | ***(1154)*** |
| **Net (decrease) / increase in cash and cash equivalents** | **(12848)** | **10604**  | **(41165)** | **(29484)** |
| Currency effect cash and cash equivalents | (34) | (173) | (1360) | (40) |
| Cash and cash equivalents, at beginning of the period | 119765  | 78970  | 149408  | 118925  |
| **Cash and cash equivalents at the end of the period** | **106883**  | **89401**  | **106883**  | **89401**  |

---

------