☒ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the fiscal year endedDecember 31,2024OR ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 For the transition period fromtoCommission file number:001-38787 CYCLERION THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Massachusetts(State or other jurisdiction ofincorporation or organization)83-1895370(I.R.S. EmployerIdentification No.)245 First Street, 18Floor,Cambridge,Massachusetts(Address of principal executive offices)02142(Zip Code)th (857)327-8778Registrant’s telephone number, including area codeSecurities registered pursuant to Section 12(b) of the Act: Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes☐No☒ Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes☐No☒ Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during thepreceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past90 days.Yes☒No☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of RegulationS-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).Yes☒No☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerginggrowth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2of the Exchange Act: Large accelerated filer☐Non-accelerated filer☒ Accelerated filer☐Smaller reporting company☒Emerging growth company☐ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revisedfinancial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control overfinancial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its auditreport.☐If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflect the correction of an error to previously issued financial statements.☐Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b).☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).Yes☐No☒ The aggregate market value of the common stock held by non-affiliates of the registrant, as of June 30, 2024, the last business day of the registrant’s most recentlycompleted second fiscal quarter, was approximately $4.8million, computed using the closing price on that day of $2.30.As of February 28, 2025, there were2,710,096shares of common stock outstanding. DOCUMENTS INCORPORATED BY REFERENCE Portions of the registrant’s definitive Proxy Statement, to be filed pursuant to Regulation 14A under the Securities Exchange Act of 1934, for its 2025 AnnualMeeting of Stockholders are incorporated by reference in Part III of this Form 10-K. TABLE OF CONTENTS PART I Item 1.Business.Item 1A.Risk Factors.Item 1B.Unresolved Staff Comments.Item 1C.CybersecurityItem 2.PropertiesItem 3.Legal ProceedingsItem 4.Mine Safety Disclosures. PART II Item 5.Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of EquitySecurities.52Item 6.Selected Financial Data.52Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations.53Item 7A.Quantitative and Qualitative Disclosures About Market Risk.60Item 8.Financial Statements and Supplementary Data.60Item 9.Changes in and Disagreements with Accountants on Accounting and Financial Disclosure.60Item 9A.Controls and Procedures.60Item 9B.Other Information.62Item 9C.Disclosure Regarding Foreign Jurisdictions That Prevent Inspections.62 PART III Item 10.Directors, Executive Officers and Corporate Governance.63Item 11.Executive Compensation.63Item 12.Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters.63Item