UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

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 Ended September 30, 2025

☐

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)

Delaware		33-0336973
(State or other jurisdiction of incorporation or organization)		(IRS Employer Identification No.)

2855 Gazelle Court, Carlsbad, California		92010
(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:


Title of each class	Trading symbol	Name of each exchange on which registered
Common Stock, $.001 Par Value	“IONS”	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 the Securities Exchange Act of 1934 during the 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 the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation 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, 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 Rule 12b-2 of the Exchange Act.


Large Accelerated Filer ☒	Accelerated Filer ☐

Non-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 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 of 1934). Yes ☐ No ☒

The number of shares of voting common stock outstanding as of October 23, 2025 was 161,974,393.

IONIS PHARMACEUTICALS, INC.

FORM 10-Q

INDEX


PART I	FINANCIAL INFORMATION

ITEM 1:	Financial Statements:

	Condensed Consolidated Balance Sheets as of September 30, 2025 (unaudited) and December 31, 2024	3

	Condensed Consolidated Statements of Operations for the three and nine months ended September 30, 2025 and 2024 (unaudited)	4

	Condensed Consolidated Statements of Comprehensive Loss for the three and nine months ended September 30, 2025 and 2024 (unaudited)	5

	Condensed Consolidated Statements of Stockholders’ Equity for the three and nine months ended September 30, 2025 and 2024 (unaudited)	6

	Condensed Consolidated Statements of Cash Flows for the nine months ended September 30, 2025 and 2024 (unaudited)	8

	Notes to Condensed Consolidated Financial Statements (unaudited)	9

ITEM 2:	Management’s Discussion and Analysis of Financial Condition and Results of Operations:

	Overview	23

	Critical Accounting Estimates	25

	Results of Operations	26

	Liquidity and Capital Resources	31

ITEM 3:	Quantitative and Qualitative Disclosures about Market Risk	33

ITEM 4:	Controls and Procedures	33

PART II	OTHER INFORMATION	34

ITEM 1:	Legal Proceedings	34

ITEM 1A:	Risk Factors	34

ITEM 2:	Unregistered Sales of Equity Securities and Use of Proceeds	52

ITEM 3:	Default upon Senior Securities	52

ITEM 4:	Mine Safety Disclosures	52

ITEM 5:	Other Information	52

ITEM 6:	Exhibits	53

SIGNATURES		54

TRADEMARKS

“Ionis,” the Ionis logo, and other trademarks or service marks of Ionis Pharmaceuticals, Inc. appearing in this report are the property 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 trade names, trademarks and service marks of others, which are the property of their respective owners. Solely for convenience, trademarks and trade names referred to in this report may appear without the ® or TM symbols.

PART I — FINANCIAL INFORMATION

ITEM 1.

FINANCIAL STATEMENTS

IONIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share data)


		September 30,			December 31,
		2025			2024
		(unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	338,341		$	242,077
Short-term investments		1,901,830			2,055,579
Contracts receivable		24,608			92,188
Inventories		10,470			12,512
Other current assets		243,744			217,934
Total current assets		2,518,993			2,620,290
Property, plant and equipment, net		106,117			94,251
Right-of-use assets		241,993			161,856
Deposits and other assets		165,988			127,278
Total assets	$	3,033,091		$	3,003,675

LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	14,326		$	42,964
Accrued compensation		57,019			69,614
Accrued liabilities		99,310			108,438
Income taxes payable		101			34
0 percent convertible senior notes, net		630,911			-
Current portion of deferred contract revenue		76,986			78,989
Other current liabilities		24,803			9,279
Total current liabilities		903,456			309,318
Long-term deferred contract revenue		107,906			156,504
1.75 percent convertible senior notes, net		567,123			565,026
0 percent convertible senior notes, net		-			628,535
Liability related to sale of future royalties, net		545,182			542,212
Long-term lease liabilities		262,672			161,805
Long-term obligations		28,785			51,924
Total liabilities		2,415,124			2,415,324
Stockholders’ equity:
Common stock, $0.001 par value; 300,000,000 shares authorized, 161,137,930 and 157,908,815 shares issued and outstanding at September 30, 2025 and December 31, 2024, respectively		161			158
Additional paid-in capital		3,045,585			2,868,812
Accumulated other comprehensive income		(25,978	)		(30,811	)
Accumulated deficit		(2,401,801	)		(2,249,808	)
Total stockholders' equity		617,967			588,351
Total liabilities and stockholders’ equity	$	3,033,091		$	3,003,675

See accompanying notes.

IONIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except per share amounts)

(Unaudited)


	Three Months Ended						Nine Months Ended
	September 30,						September 30,
		2025			2024			2025			2024
Revenue:
Commercial revenue:
Product sales, net	$	31,792		$	-		$	57,353		$	-
Royalty revenue		75,694			66,807			209,811			180,036
Other commercial revenue		8,112			8,924			27,359			27,324
Total commercial revenue		115,598			75,731			294,523			207,360
Research and development revenue:
Collaborative agreement revenue		31,436			44,883			413,387			235,753
WAINUA joint development revenue		9,685			13,200			32,471			35,449
Total research and development revenue		41,121			58,083			445,858			271,202
Total revenue		156,719			133,814			740,381			478,562

Expenses:
Cost of sales		2,338			1,071			7,952			7,385
Research, development and patent		217,754			219,761			635,973			656,040
Selling, general and administrative		96,809			61,638			263,681			179,395
Total operating expenses		316,901			282,470			907,606			842,820

Loss from operations		(160,182	)		(148,656	)		(167,225	)		(364,258	)

Other income (expense):
Investment income		23,682			26,228			73,035			78,112
Interest expense		(4,212	)		(4,161	)		(12,434	)		(12,803	)
Interest expense related to sale of future royalties		(17,952	)		(18,533	)		(55,422	)		(54,788	)
Gain (loss) on investments, net		29,908			879			9,432			(321	)
Other income, net		363			142			929			1,029

Loss before income tax benefit (expense)		(128,393	)		(144,101	)		(151,685	)		(353,029	)

Income tax benefit (expense)		(213	)		3,621			(308	)		3,481

Net loss	$	(128,606	)	$	(140,480	)	$	(151,993	)	$	(349,548	)

Basic and diluted net loss per share		(0.80	)	$	(0.95	)	$	(0.95	)	$	(2.38	)
Shares used in computing basic and diluted net loss per share		159,765			148,593			159,216			146,703

See accompanying notes.

IONIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(in thousands)

(Unaudited)


	Three Months Ended						Nine Months Ended
	September 30,						September 30,
		2025			2024			2025			2024
Net loss	$	(128,606	)	$	(140,480	)	$	(151,993	)	$	(349,548	)
Unrealized gains on debt securities, net of tax		2,091			10,315			4,088			8,259
Currency translation adjustment		(82	)		350			745			213
Comprehensive loss	$	(126,597	)	$	(129,815	)	$	(147,160	)	$	(341,076	)

See accompanying notes.

IONIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY

(in thousands)

(Unaudited)


	Common Stock					Additional		Accumulated Other						Total
Description		Shares		Amount		Paid in Capital		Comprehensive Loss			Accumulated Deficit			Stockholders' Equity
Balance at June 30, 2024		146,025	$	146	$	2,303,369	$	(34,838	)	$	(2,004,979	)	$	263,698
Net loss		-		-		-		-			(140,480	)		(140,480	)
Change in unrealized gains, net of tax		-		-		-		10,315			-			10,315
Foreign currency translation		-		-		-		350			-			350
Issuance of common stock in connection with employee stock plans, net		288		-		7,002		-			-			7,002
Issuance of public common stock, net		11,500		12		489,081		-			-			489,093
Stock-based compensation expense		-		-		32,490		-			-			32,490
Balance at September 30, 2024		157,813	$	158	$	2,831,942	$	(24,173	)	$	(2,145,459	)	$	662,468

Balance at June 30, 2025		159,197	$	159	$	2,932,747	$	(27,987	)	$	(2,273,195	)	$	631,724
Net loss		-		-		-		-			(128,606	)		(128,606	)
Change in unrealized gains, net of tax		-		-		-		2,091			-			2,091
Foreign currency translation		-		-		-		(82	)		-			(82	)
Issuance of common stock in connection with employee stock plans, net		1,941		2		81,257		-			-			81,259
Stock-based compensation expense		-		-		31,581		-			-			31,581
Balance at September 30, 2025		161,138	$	161	$	3,045,585	$	(25,978	)	$	(2,401,801	)	$	617,967

See accompanying notes.

IONIS PHARMACEUTICALS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY

(in thousands)

(Unaudited)


	Common Stock					Additional		Accumulated Other						Total
Description		Shares		Amount		Paid in Capital		Comprehensive Loss			Accumulated Deficit			Stockholders' Equity
Balance at December 31, 2023		144,341	$	144	$	2,215,098	$	(32,645	)	$	(1,795,911	)	$	386,686
Net loss		-		-		-		-			(349,548	)		(349,548	)
Change in unrealized gains, net of tax		-		-		-		8,259			-			8,259
Foreign currency translation		-		-		-		213			-			213
Issuance of common stock in connection with employee stock plans, net		1,972		2		33,205		-			-			33,207
Issuance of public common stock, net		11,500		12		489,081		-			-			489,093
Stock-based compensation expense		-		-		94,558		-			-			94,558
Balance at September 30, 2024		157,813	$	158	$	2,831,942	$	(24,173	)	$	(2,145,459	)	$	662,468

Balance at December 31, 2024		157,909	$	158	$	2,868,812	$	(30,811	)	$

SEC Form 10-Q filed by Ionis Pharmaceuticals Inc.