Stoke Therapeutics reported a $73.64 million net loss

Item 6.

Exhibits

71

Signatures

72

2

FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements within the safe harbor provisions for forward-looking statements contained in Section 27A of the Securities Act of 1933, as amended (the "Securities Act") and Section 21E of the Securities Exchange Act of 1934, as amended (the "Exchange Act"). All statements other than statements of present and historical facts contained in this Quarterly Report on Form 10-Q, including, but not limited to, statements regarding the ability of zorevunersen (STK-001) to treat the underlying causes of Dravet syndrome and reduce seizures or show improvements in behavior or cognition at the indicated dosing levels or at all, the design, timing and results of clinical studies (including our EMPEROR Phase 3 study and our OSPREY Phase 1 study), enrollment timelines, data readouts, and regulatory submissions or decisions, our efforts to expand our pipeline using our proprietary protein upregulation platform, the receipt of potential milestone or royalty payments or the exercise of options under our collaboration agreement with Biogen International GmbH ("Biogen") and our collaboration agreement with Acadia Pharmaceuticals Inc. ("Acadia"), our future results of operations and financial position, business strategy, prospective products, planned preclinical studies and clinical or field trials, regulatory approvals, research and development costs, and timing and likelihood of success, as well as plans and objectives of management for future operations, may be forward-looking statements. In some cases, you can identify forward-looking statements by terms such as "may," "will," "should," "expect," "plan," "anticipate," "could," "intend," "target," "project," "contemplate," "believe," "estimate," "predict," "potential" or "continue" or the negative of these terms or other similar expressions, although not all forward-looking statements contain these words.

Forward-looking statements are based on our management's beliefs and assumptions and on information currently available to us.^{1 1}Such statements are subject to a number of known and unknown risks, uncertainties and assumptions, and actual results may differ materially from those expressed or implied in the forward-looking statements due to various factors, including, but not limited to, those identified in Part I. Item 2.^{1 1}"Management's Discussion and Analysis of Financial Condition and Results of Operations" and Part II.^{1 1}Item 1A "Risk Factors.¹" These risks and uncertainties include, but are not limited to:

• our ability to become profitable or procure sufficient funding and our limited operating history;

• our ability to develop, obtain regulatory approval for and commercialize zorevunersen, STK-002 and our future product candidates;

• our success in early preclinical studies or clinical trials, which may not be indicative of results obtained in later studies or trials;

• the success of our collaborations with Acadia and Biogen and our ability to enter into successful collaborations in the future;

• the availability of coverage and adequate reimbursement from third party payors for zorevunersen, STK-002 and our future product candidates, if such products are approved;

• our ability to identify patients with the diseases treated by zorevunersen, STK-002 or our future product candidates, and to enroll patients in trials;

• the success of our efforts to use our proprietary protein upregulation platform to expand our pipeline of product candidates and develop marketable products;

• the direct and indirect impact of inflation, interest rates, foreign currency exchange rates, tariffs, instability in the global banking system, geopolitical conflict and macroeconomic conditions, including as a result of a potential temporary federal government shutdown, on our business, financial condition and operations, including on our expenses, supply chain, strategic partners, research and development costs, clinical trials and employees;

• our ability to obtain, maintain and protect our intellectual property;

• our reliance upon intellectual property licensed from third parties;

• our ability to identify, recruit and retain key personnel;

• our financial performance; and

• developments or projections relating to our competitors or our industry.

You should read this Quarterly Report on Form 10-Q and the documents that we reference herein completely and with the understanding that our actual future results may be materially different from what we expect. We qualify all of our forward-looking statements by these cautionary statements. Except as required by applicable law, we do not plan to publicly update or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise.

3

PART I—FINANCI AL INFORMATION

Item 1. Financi al Statements.

Stoke Therapeutics, Inc.

Condensed consolidated ba lance sheets (in thousands, except share and per share amounts) (unaudited)

September 30,

December 31,

2026

2025

Assets

Current assets:

Cash and cash equivalents

$

107,271

$

84,220

Marketable securities - current

211,916

200,450

Accounts receivable

8,543

5,936

Prepaid expenses

17,596

8,736

Interest receivable

1,533

1,969

Other current assets

7,558

4,389

Total current assets

$

354,417

$

305,700

Marketable securities - long-term

39,602

106,260

Restricted cash - long-term

3,227

227

Operating lease right-of-use assets

1,233

3,101

Property and equipment, net

8,213

3,146

Total assets²

$²

406,692²

$

418,434

Liabilities and stockholders' equity

Current liabilities:

Accounts payable

$

4,029

$

4,939

Accrued and other current liabilities

38,584

41,035

Deferred revenue - current portion

6,364

11,901

Total current liabilities

$

48,977

$

57,875

Deferred revenue - net of current portion

4,446

6,961

Other long-term liabilities

681

1,141

Total long-term liabilities

5,127

8,102

Total liabilities²

$²

54,104²

$

65,977

Commitments and contingencies (Note 6)

Stockholders' equity

Common stock, par value of $ 0.0001 per share; 300,000,000 shares authorized, 64,813,537 and 58,921,999 shares issued and outstanding as of September 30, 2026 and December 31, 2025, respectively

6

5

Additional paid-in capital

1,036,612

849,624

Accumulated other comprehensive (loss) income

( 1,050

)

543

Accumulated deficit

( 682,980

)

( 497,715

)

Total stockholders' equity

$

352,588

$

352,457

Total liabilities and stockholders' equity

$

406,692

$

418,434

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

4

Stoke Therapeutics, Inc.

Condensed consolidated stateme nts of operations and comprehensive (loss) income (in thousands, except share and per share amounts) (unaudited)

Three Months Ended September 30,

Nine Months Ended September 30,

2026

2025

2026

2025

Revenue

$

11,255

$

10,632

$

26,808

$

183,018

Operating expenses:

Research and development

59,831

37,696

149,004

96,227

Sales, general and administrative

28,739

16,027

73,966

45,942

Total operating expenses

88,570

53,723

222,970

142,169

(Loss) income from operations

( 77,315

)

( 43,091

)

( 196,162

)

40,849

Other income (expense):

Interest income (expense), net

3,665

3,463

10,564

10,141

Other income

6

3

333

59

Total other income (expense)

3,671

3,466

10,897

10,200

(Loss) income before income taxes

$

( 73,644

)

$

( 39,625

)

$

( 185,265

)

$

51,049

Provision for income taxes

—

( 1,278

)

—

—

Net (loss) income

$

( 73,644

)

$

( 38,347

)

$

( 185,265

)

$

51,049

Net (loss) income per share:

Basic

$

( 1.08

)

$

( 0.65

)

$

( 2.81

)

$

0.88

Diluted

( 1.08

)

( 0.65

)

( 2.81

)

0.85

Weighted-average common shares outstanding:

Basic

68,362,880

58,611,677

65,834,172

58,278,812

Diluted

68,362,880

58,611,677

65,834,172

60,397,681

Comprehensive (loss) income:

Net (loss) income

$

( 73,644

)

$

( 38,347

)

$

( 185,265

)

$

51,049

Other comprehensive (loss) gain:

Unrealized (loss) gain on marketable securities

( 508

)

350

( 1,593

)

597

Total other comprehensive (loss) gain

$

( 508

)

$

350

$

( 1,593

)

$

597

Comprehensive (loss) income

$

( 74,152

)

$

( 37,997

)

$

( 186,858

)

$

51,646

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

5

Stoke Therapeutics, Inc.

Condensed c onsolidated statements of stockholders' equity (in thousands, except share and per share amounts) (unaudited)

Common Stock

Additional paid-in capital

Accumulated other comprehensive gain (loss)

Accumulated deficit

Total stockholders' equity

Shares

Amount

Balance as of December 31, 2024

54,032,826

$

5

$

719,997

$

( 151

)

$

( 490,830

)

$

229,021

Unrealized gain on marketable securities

—

—

—

47

—

47

Stock-based compensation

—

—

6,753

—

—

6,753

Issuance of common stock upon exercise of stock options

214,996

—

1,004

—

—

1,004

Issuance of common stock related to employee stock purchase plan

39,467

—

370

—

—

370

Issuance of vested restricted and performance stock units

308,425

—

—

—

—

—

Net income

—

—

—

—

112,879

112,879

Balance as of March 31, 2025

54,595,714

$

5

$

728,124

$

( 104

)

$

( 377,951

)

$

350,074

Unrealized gain on marketable securities

—

—

—

200

—

200

Stock-based compensation

—

—

7,598

—

—

7,598

Issuance of common stock upon exercise of stock options

126,531

—

554

—

—

554

Issuance of vested restricted and performance stock units

1,210

—

—

—

—

—

Net loss

—

—

—

—

( 23,483

)

( 23,483

)

Balance as of June 30, 2025

54,723,455

$

5

$

736,276

$

96

$

( 401,434

)

$

334,943

Unrealized gain on marketable securities

—

—

—

350

—

350

Stock-based compensation

—

—

8,039

—

—

8,039

Issuance of common stock upon exercise of stock options

262,320

—

2,488

—

—

2,488

Issuance of vested restricted and performance stock units

68,210

—

—

—

—

—

Issuance of common stock related to employee stock purchase plan

66,017

—

632

—

—

632

Net loss

—

—

—

—

( 38,347

)

( 38,347

)

Balance as of September 30, 2025

55,120,002

$

5

$

747,435

$

446

$

( 439,781

)

$

308,105

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

6

Stoke Therapeutics, Inc.

Condensed consolidated statements of stockholders' equity (in thousands, except share and per share amounts) (unaudited)

Common Stock

Additional paid-in capital

Accumulated other comprehensive gain (loss)

Accumulated deficit

Total stockholders' equity

Shares

Amount

Balance as of December 31, 2025

58,921,999

$

5

$

849,624

$

543

$

( 497,715

)

$

352,457

Unrealized (loss) on marketable securities

—

—

—

( 658

)

—

( 658

)

Stock-based compensation

—

—

8,753

—

—

8,753

Issuance of common stock upon exercise of stock options

260,554

—

3,205

—

—

3,205

Issuance of common stock related to employee stock purchase plan

46,994

465

—

—

465

Issuance of vested restricted and performance stock units

443,786

—

—

—

—

—

Shares sold as part of controlled equity offering sales agreement

2,567,014

1

80,657

—

—

80,658

Net loss

—