UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





FORM 10-K/A

Amendment No. 1





(Mark One)

|☒ | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the fiscal year ended December 31, 2017

OR



|☐ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period
from
to

Commission File Number: 001-38311





Denali Therapeutics Inc.

(Exact name of registrant as specified in its charter)







|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 46-3872213                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer
Identification No.)

151 Oyster Point Blvd., 2nd Floor

South San Francisco, CA, 94080

(Address of principal executive offices and zip code)

(650) 866-8548

(Registrants telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:



|                                        |  |                                          
|--------------------------------------- |  | -----------------------------------------
|Title of each
class                     |  | Name of each exchange on
which registered
|Common stock, par value $0.01 per share |  | The NASDAQ Global Select Market          

Securities registered pursuant to Section 12(g) of the Act: None





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 Securities Exchange 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 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 and posted on its corporate Web site, if any, 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 and post such files).    Yes  ☒    No  ☐

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K
(§229.405 of this chapter) is not contained herein, and will not be contained, to the best of registrants knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  ☐

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 Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |                                                  |  |                           |  |  
|----------------------- |  | ------------------------------------------------ |  | ------------------------- |  | -
|Large accelerated filer |  | ☐                                                |  | Accelerated filer         |  | ☐
|                        |  |                                                  | 
|Non-accelerated filer   |  | ☒  (Do not check if a smaller reporting company) |  | 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 12b-2 of the
Exchange Act).    Yes  ☐    No  ☒

The aggregate market value of
the common stock held by non-affiliates of the registrant, based on the closing price of a share of common stock on December 8, 2017 as reported by the NASDAQ Global Select Market on such date was
approximately $628.4 million. The registrant has elected to use December 8, 2017, which was the initial trading date on the NASDAQ Global Select Market, as the calculation date because on June 30, 2017, the registrant was a privately
held company. Shares of the registrants common stock held by each executive officer, director and holder of 5% or more of the outstanding common stock have been excluded in that such persons may be deemed to be affiliates. This calculation
does not reflect a determination that certain persons are affiliates of the registrant for any other purpose.

The number of outstanding
shares of the registrants common stock as of March 12, 2018 was 94,429,245.

DOCUMENTS INCORPORATED BY REFERENCE:

Portions of the registrants Definitive Proxy Statement relating to the registrants 2018 Annual Meeting of Stockholders are
incorporated by reference into Part III of this Annual Report on Form 10-K where indicated. Such Definitive Proxy Statement was filed with the Securities and Exchange Commission within 120 days after the end
of the registrants 2017 fiscal year ended December 31, 2017.









---

EXPLANATORY NOTE

Denali Therapeutics Inc. (the Company) is filing this Amendment No. 1 on
Form 10-K/A (Amendment) to amend its Annual Report on Form 10-K for the year ended December 31, 2017 (the
Form 10-K), which was originally filed with the Securities and Exchange Commission on March 19, 2018. The purpose of this Amendment is to refile Exhibit 10.16, which was originally
filed with the Form 10-K, with revised redactions in response to comments received from the staff of the Securities and Exchange Commission on the confidential treatment request filed by the Company
with respect to Exhibit 10.16.

This Amendment speaks as of the original filing date and does not reflect events occurring after the
filing of the Form 10-K or modify or update disclosures that may be affected by subsequent events. No revisions are being made to the Companys financial statements or any other disclosure contained
in the Form 10-K.

This Amendment is an exhibit-only filing. Except for the changes to
Exhibit 10.16, this Amendment does not otherwise update any exhibits as originally filed or previously amended.

In addition, as required
by Rule 12b-15 under the Securities Exchange Act of 1934, as amended (the Exchange Act), new certifications by the Companys principal executive officer and principal financial
officer are filed herewith as exhibits to this Amendment pursuant to Rule 13a-14(a) and 15d-14(a) of the Exchange Act. The Company is not including
certifications pursuant to Section 1350 of Chapter 63 of Title 18 of the United States Code (18 U.S.C. 1350) as no financial statements are being filed with this Amendment.



---

PART IV

ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

(a) The following documents are filed as part of this report:

1. Financial Statements

The
consolidated financial statements of the Company were previously submitted with the original filing of this Form 10-K.

2. Financial Statement Schedules

All schedules are omitted because they are not applicable or the required information is shown in the financial statements or notes thereto.

3. Exhibits

The documents
listed in the Exhibit Index are incorporated by reference or are filed with this report, in each case as indicated therein (numbered in accordance with Item 601 of Regulation S-K).



---

EXHIBIT INDEX



|               |  |                                                                                                                                                                                                                     |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 
|-------------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- | ----- |  | -------- |  | ---------- | ------ |  |  | ----------- |  |  |  | ---------- | 
|               |  |                                                                                                                                                                                                                     |  | Incorporated by Reference |      
|Exhibit
Number |  | Description                                                                                                                                                                                                         |  | Form                      |       |  | File No. |  |            | Number |  |  | Filing Date | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|3.1            |  | Amended and Restated Certificate of Incorporation of the Registrant.                                                                                                                                                |  |                           | 8-K   |  |          |  | 001-38311  |        |  |  | 3.1         |  |  |  | 12/12/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|3.2            |  | Amended and Restated Bylaws of the Registrant.                                                                                                                                                                      |  |                           | 8-K   |  |          |  | 001-38311  |        |  |  | 3.2         |  |  |  | 12/12/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|4.1            |  | Investors Rights Agreement among the Registrant and certain of its stockholders, dated May 8, 2015, as amended on June 
4, 2015, July 22, 2015 and June 22, 2016.                                                  |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 4.1         |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|4.2            |  | Specimen common stock certificate of the Registrant.                                                                                                                                                                |  |                           | S-1/A |  |          |  | 333-221522 |        |  |  | 4.2         |  |  |  | 11/27/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.1+          |  | Form of Indemnification Agreement between the Registrant and each of its directors and executive officers.                                                                                                          |  |                           | S-1/A |  |          |  | 333-221522 |        |  |  | 10.1        |  |  |  | 11/27/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.2+          |  | 2015 Stock Incentive Plan, as amended, and forms of agreement thereunder.                                                                                                                                           |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.2        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.3+          |  | 2017 Equity Incentive Plan and forms of agreements thereunder.                                                                                                                                                      |  |                           | S-1/A |  |          |  | 333-221522 |        |  |  | 10.3        |  |  |  | 11/27/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.4+          |  | 2017 Employee Stock Purchase Plan and form of agreement thereunder.                                                                                                                                                 |  |                           | S-1/A |  |          |  | 333-221522 |        |  |  | 10.4        |  |  |  | 12/7/2017  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.5+          |  | Offer Letter between the Registrant and Ryan J. Watts, Ph.D., dated November 10, 2017.                                                                                                                              |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.5        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.6+          |  | Offer Letter between the Registrant and Alexander O. Schuth, M.D., dated November 10, 2017.                                                                                                                         |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.6        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.7+          |  | Offer Letter between the Registrant and Steve E. Krognes, dated November 10, 2017.                                                                                                                                  |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.7        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.8+          |  | Offer Letter between the Registrant and Carole Ho, M.D., dated November 10, 2017.                                                                                                                                   |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.8        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.9           |  | Lease Agreement between the Registrant and HCP Oyster Point III LLC, dated September 24, 2015.                                                                                                                      |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.9        |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.10Ü         |  | Exclusive License Agreement between the Registrant and Genentech, Inc., dated June 17, 2016.                                                                                                                        |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.10       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.11Ü         |  | License and Collaboration Agreement between the Registrant, F-star Gamma Limited, f-star Biotechnologische Forschungs-und Entwicklungsges m.b.H. and F-star Biotechnology Limited, dated August 24, 2016.           |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.11       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.12Ü         |  | Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 
6, 2017, as amended by Amendment No. 1 on October 18, 2017.                                            |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.12       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.12.1#       |  | Amendment No. 2 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 
6, 2017, as amended by Amendment No. 1 on October 18, 2017, dated January 18, 2018. |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 10.12.1     |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.13+         |  | Key Executive Change in Control and Severance Plan.                                                                                                                                                                 |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.13       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.14+         |  | Executive Incentive Compensation Plan.                                                                                                                                                                              |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.14       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.15+         |  | Outside Director Compensation Policy.                                                                                                                                                                               |  |                           | S-1   |  |          |  | 333-221522 |        |  |  | 10.15       |  |  |  | 11/13/2017 | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.16#         |  | Option and Collaboration Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated January 3, 2018.                                                                                         |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.17          |  | Common Stock Purchase Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated January 3, 2018.                                                                                            |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 10.17       |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|10.18          |  | Standstill and Stock Restriction Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated February 
23, 2018.                                                                              |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 10.18       |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|23.1           |  | Consent of Independent Registered Public Accounting Firm.                                                                                                                                                           |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 23.1        |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|31.1           |  | Certification of Chief Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 31.1        |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|31.2           |  | Certification of Chief Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           | 10-K  |  |          |  | 001-38311  |        |  |  | 31.2        |  |  |  | 3/19/2018  | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|31.3           |  | Certification of Chief Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|31.4           |  | Certification of Chief Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|32.1^          |  | Certification of Chief Executive Officer pursuant to Section 906 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 
|               |  |                                                                                                                                                                                                                     |  |                           |      
|32.2^          |  | Certification of Chief Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act.                                                                                                                         |  |                           |       |  |          |  |            |        |  |  |             |  |  |  |            | 



|Ü | Portions of the exhibit have been omitted pursuant to an order granted by the Securities and Exchange Commission for confidential treatment.
|- | --------------------------------------------------------------------------------------------------------------------------------------------

|# | Portions of this exhibit have been omitted pursuant to a request for confidential treatment and this exhibit has been filed separately with the SEC.
|- | ----------------------------------------------------------------------------------------------------------------------------------------------------

|+ | Indicates management contract or compensatory plan.
|- | ---------------------------------------------------

|^ | Previously furnished with the Registrants Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 19, 2018. The information in this
exhibit is deemed furnished and not filed with the Securities and Exchange Commission and is not to be incorporated by reference into any filing of the Registrant under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934,
as amended, whether made before or after the hereof, irrespective of any general incorporation language contained in such filing.
|- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



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ITEM 16. FORM 10-K SUMMARY

None.



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SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this Amendment
No. 1 to its Annual Report on Form 10-K to be signed on its behalf by the undersigned, thereunto duly authorized.

Date: July 13, 2018



DENALI THERAPEUTICS INC.By:

/s/ Ryan J. WattsRyan J. Watts, Ph.D.President and Chief Executive Officer