Company: DNLI
Filing Date: 2025-12-10
Form Type: 424B5
Source: 0001628280-25-056361
Chunk: 9

Company: Denali Therapeutics Inc.
Filing Date: 2025-12-10
Form: 424B5
Chunk 9
---
 Equity Incentive Plan, or the 2017 Plan, as of September 30, 2025, plus any future increases in the number of shares of common stock reserved for issuance under the 2017 Plan pursuant to the evergreen provision of the 2017 Plan;

• 7,668,813 shares of common stock reserved for future issuance under our 2017 Employee Stock Purchase Plan, or the 2017 ESPP, as of September 30, 2025, plus any future increases in the number of shares of common stock reserved for issuance under the 2017 ESPP pursuant to the evergreen provision of the 2017 ESPP; and

• pre-funded warrants to purchase up to 2,285,714 shares of our common stock at an exercise price of $0.01 per share.

Except as otherwise indicated, all information in this prospectus supplement assumes:

• no exercise by the underwriters of their option to purchase up to 1,714,285 additional shares of common stock in this offering;

• no exercise of the pre-funded warrants that we are offering in this offering in lieu of common stock to certain investors; and

• no exercise or settlement of stock options, RSUs or other equity awards described above, no grant of additional awards under our 2017 Plan, and no issuance of shares under the 2017 ESPP, in each case, after September 30, 2025.

<div align='center'>S-6</div>

### RISK FACTORS
Investing in our securities involves a high degree of risk. Prior to making a an investment decision, you should carefully consider the risks discussed below and discussed in Part I, Item 1A “Risk Factors” in our most recent Annual Report on Form 10-K and Part II, Item 1A “Risk Factors” in our Quarterly Reports on Form 10-Q, each as may be amended, supplemented or superseded from time to time by other reports we file with the SEC in the future, all of which are incorporated by reference into this prospectus supplement and the accompanying prospectus in their entirety, together with other information in this prospectus supplement and the accompanying prospectus, including any information incorporated or deemed to be incorporated by reference herein. The risks and uncertainties we have described are not the only ones facing us. Additional risks and uncertainties not presently known to us, or that we currently see as immaterial, may also harm our business. If any of these risks occur, our business, financial