Form 10-Q (Mark One) ☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the Quarterly Period EndedJune 30, 2026 OR ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF SECURITIES EXCHANGE ACT OF 1934 For the transition period from _____ to _____ Commission file number 000-19125 Ionis Pharmaceuticals, Inc. (Exact name of Registrant as specified in its charter) Delaware33-0336973(State or other jurisdiction of incorporation or organization)(IRS Employer Identification No.) 2855 Gazelle Court, Carlsbad, California92010(Address of Principal Executive Offices)(Zip Code) 760-931-9200(Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: Name of each exchange on which registered The Nasdaq Stock Market LLC Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of theSecurities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file suchreports), and (2) has been subject to such filing requirements for the past 90 days. Yes☒No☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submittedand posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter periodthat 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, smallerreporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smallerreporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. Large Accelerated Filer☒ Accelerated Filer☐ Smaller Reporting Company☐Emerging Growth Company☐ Non-accelerated Filer☐ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period forcomplying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12(b)-2 of the Securities Exchange Act of1934). Yes☐No☒ The number of shares of voting common stock outstanding as of July 23, 2026 was 166,184,322. IONIS PHARMACEUTICALS, INC.FORM 10-QINDEX PART IFINANCIAL INFORMATIONITEM 1:Financial Statements:Condensed Consolidated Balance Sheetsas ofJune 30, 2026(unaudited) and December 31,20253Condensed Consolidated Statements of Operationsfor the three and six months endedJune 30, 2026 and 2025(unaudited)4Condensed Consolidated Statements of Comprehensive Income (Loss)for the three and six months ended June30, 2026 and 2025 (unaudited)5Condensed Consolidated Statements of Stockholders’ Equityfor the three and six months ended June 30, 2026and 2025 (unaudited)6Condensed Consolidated Statements of Cash Flowsfor the six months ended June 30, 2026 and 2025(unaudited)8Notes to Condensed Consolidated Financial Statements (unaudited)9ITEM 2:Management’s Discussion and Analysis of Financial Condition and Results of Operations:Overview27Critical Accounting Estimates30Results of Operations30Liquidity and Capital Resources36ITEM 3:Quantitative and Qualitative Disclosures about Market Risk38ITEM 4:Controls and Procedures38PART IIOTHER INFORMATION39ITEM 1:Legal Proceedings39ITEM 1A:Risk Factors39ITEM 2:Unregistered Sales of Equity Securities and Use of Proceeds58ITEM 3:Default upon Senior Securities58ITEM 4:Mine Safety Disclosures58ITEM 5:Other Information58ITEM 6:Exhibits59SIGNATURES60TRADEMARKS “Ionis,” the Ionis logo, and other trademarks or service marks of Ionis Pharmaceuticals, Inc. appearing in this report are theproperty of Ionis Pharmaceuticals, Inc. “Akcea,” the Akcea logo, and other trademarks or service marks of Akcea Therapeutics, Inc.appearing in this report are the property of Akcea Therapeutics, Inc., Ionis’ wholly owned subsidiary. This report contains additional tradenames, trademarks and service marks of others, which are the property of their respective owners. Solely for convenience, trademarksand trade names referred to in this report may appear without the ® or TM symbols. Table of Contents IONIS PHARMACEUTICALS, INC.CONDENSED CONSOLIDATED BALANCE SHEETS(in thousands, except share data) Cash and cash equivalents$350,065$372,260Short-term investments1,704,5202,305,176Contracts receivable58,84566,059Inventories50,83310,048Other current assets327,011237,092Total current assets2,491,2742,990,635Property, plant and equipment, net155,131123,048Right-of-use assets231,560238,549Deposits and other assets116,536171,604Total assets$2,994,501$3,523,836 IONIS PHARMACEUTICALS, INC.CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS(in thousands, except per share amounts)(Unaudited) IONIS PHARMACEUTICALS