☒ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the fiscal year ended: December 31, 2025☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period fromtoCommission file number: 001-36167 KARYOPHARM THERAPEUTICS INC. (Exact name of registrant as specified in its charter) 85 Wells Avenue,2ndFloor, Newton, Massachusetts 02459(Address of principal executive offices) (zip code)Registrant’s telephone number, including area code: (617) 658-0600Securities 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 duringthe preceding 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 thepast 90 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 ofRegulation S-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, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule12b-2 of the Exchange Act. 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 Large accelerated filer☐ Non-accelerated filer☒ revised financial 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 controlover financial 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-2of the Exchange Act).Yes☐No☒The aggregate market value of the registrant’s voting and non-voting common stock held by non-affiliates of the registrant (without admitting that any person whose shares are not included in such calculation is an affiliate) computed by reference to the price at which the common stock was last sold on June 30, 2025 wasapproximately $37.0 million. Shares of common stock held by each executive officer and director and by each holder of 10% or more of the outstanding commonstock have been excluded in that such persons may be deemed to be affiliates. This determination of affiliate status is not necessarily a conclusive determination forother purposes.Number of shares outstanding of the registrant’s Common Stock as of February 5, 2026: 18,343,968. Documents incorporated by reference: Portions of the registrant’s Proxy Statement for its 2026 Annual Meeting of Stockholders, which the registrant intends to file with the Securities and Exchange Commission no later than 120 days after the registrant’s fiscal year end of December 31, 2025, are incorporated by reference into Part III of this Annual Report onForm 10-K. TABLE OF CONTENTS PART I 6Item 1.Business6Item 1A.Risk Factors54Item 1B.Unresolved Staff Comments105Item 1C.Cybersecurity105Item 2.Properties107Item 3.Legal Proceedings107Item 4.Mine Safety Disclosures107PART II108Item 5.Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases ofEquity Securities108Item 6.[Reserved]108Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations109Item 7A.Quantitative and Qualitative Disclosures about Market Risk118Item 8.Financial Statements and Supplementary Data118Item 9A.Controls and Procedures118Item 9B.Other Information121Item 9C.Disclosure Regarding F