Document:

EX-10.8

 Exhibit 10.8 

ANNEXON, INC. 

EMPLOYMENT AGREEMENT 

This Employment Agreement (the “Agreement”), is made and entered into by and between Annexon, Inc., a Delaware
corporation (the “Company”) and Sanjay Keswani (“Executive” and, together with the Company, the “Parties”). This Agreement will become effective as of immediately prior to the
time the Company’s registration statement relating to the initial public offering of the Company’s common stock becomes effective (the “Effective Date”). This Agreement supersedes in its entirety that certain offer
letter between Executive and the Company dated as of April 9, 2019 (“Offer Letter”). 
 WHEREAS,
the Company desires to assure itself of the continued services of Executive by engaging Executive to perform services as an employee of the Company under the terms hereof; 

WHEREAS, Executive desires to provide continued services to the Company on the terms herein provided; and 

WHEREAS, the Parties desire to execute this Agreement to supersede the Offer Letter in its entirety and reflect certain changes to
Executive’s employment with the Company effective as of the Effective Date. 
 NOW, THEREFORE, in consideration of the
foregoing, and for other good and valuable consideration, including the respective covenants and agreements set forth below, the receipt and sufficiency of which are hereby acknowledged, the Parties hereto agree as follows: 

1. Employment. 
 (a)
General. The Company shall employ Executive upon the terms and conditions provided herein effective as of the Effective Date. 

(b) Position and Duties. Effective as of the Effective Date, Executive: (i) shall continue to serve as the Company’s
Executive Vice President and Chief Medical Officer, with responsibilities, duties, and authority usual and customary for such position, subject to direction by the Chief Executive Officer of the Company (the “CEO”); (ii)
shall continue to report directly to the CEO; and (iii) agrees promptly and faithfully to comply with all present and future policies, requirements, rules and regulations, and reasonable directions and requests, of the Company in connection
with the Company’s business. At the Company’s request, Executive shall serve the Company and/or its subsidiaries and affiliates in such other capacities in addition to the foregoing as the Company shall designate, provided that such
additional capacities are consistent with Executive’s position as the Company’s Executive Vice President and Chief Medical Officer. In the event that Executive serves in any one or more of such additional capacities, Executive’s
compensation shall not automatically be increased on account of such additional service. 

  
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 (c) Principal Office. Executive shall continue to perform services for the
Company at the Company’s offices located in South San Francisco, California, or, with the Company’s consent, at any other place in connection with the fulfillment of Executive’s role with the Company; provided, however, that the
Company may from time to time require Executive to travel temporarily to other locations in connection with the Company’s business. 

(d) Exclusivity. Except with the prior written approval of the CEO (which the CEO may grant or withhold in his or her sole and
absolute discretion), Executive shall devote Executive’s best efforts and full working time, attention, and energies to the business of the Company, except during any paid vacation or other excused absence periods. Notwithstanding the
foregoing, Executive may, without violating this Section 1(d), (i) as a passive investment, own publicly traded securities in such form or manner as will not require any services by Executive in the operation of the entities in which such
securities are owned; (ii) engage in charitable and civic activities; or (iii) engage in other personal passive investment activities, in each case, so long as such interests or activities do not materially interfere to the extent such
activities do not, individually or in the aggregate, interfere with or otherwise prevent the performance of Executive’s duties and responsibilities hereunder. Executive may also serve as a member of the board of directors or board of advisors
of another organization provided (i) such organization is not a competitor of the Company; (ii) Executive receives prior written approval from the Company’s CEO; and (iii) such activities do not individually or in the aggregate
interfere with the performance of Executive’s duties under this Agreement, violate the Company’s standards of conduct then in effect, or raise a conflict under the Company’s conflict of interest policies. For the avoidance of doubt,
the CEO has approved Executive’s continued service with those organizations set forth on Exhibit A, such approval to continue until the earlier to occur of (a) the CEO’s revocation of such approval in his or her sole and
absolute discretion, or (b) such time as such service interferes with the performance of Executive’s duties under this Agreement, violates the Company’s standards of conflict or raises a conflict under the Company’s conflict of
interest policies. 
 2. Term. The period of Executive’s employment under this Agreement shall commence on the Effective Date and
shall continue until Executive’s employment with the Company is terminated pursuant to Section 5. The phrase “Term” as used in this Agreement shall refer to the entire period of employment of Executive by the
Company. 
 3. Compensation and Related Matters. 

(a) Annual Base Salary. During the Term, Executive shall receive a base salary at the rate of $407,800 per year (as may be
increased from time to time, the “Annual Base Salary”), subject to withholdings and deductions, which shall be paid to Executive in accordance with the customary payroll practices and procedures of the Company. Such Annual
Base Salary shall be reviewed by the CEO, and, as applicable, the Board of Directors of the Company (the “Board”) and/or the Compensation Committee of the Board, not less than annually. 

(b) Annual Bonus. Executive shall be eligible to receive a discretionary annual bonus based on Executive’s achievement of
performance objectives established by the Board, its Compensation Committee and/or the CEO, such bonus to be targeted at 40% of Executive’s Annual Base Salary (the “Annual Bonus”). Any Annual Bonus approved by the Board
or the Compensation Committee of the Board shall be paid at the same time annual bonuses are paid to other executives of the Company generally, subject to Executive’s continuous employment through the date of approval. 

  
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 (c) Benefits. Executive shall be entitled to participate in such employee and
executive benefit plans and programs as the Company may from time to time offer to provide to its executives, subject to the terms and conditions of such plans. Notwithstanding the foregoing, nothing herein is intended, or shall be construed, to
require the Company to institute or continue any particular plan or benefit. 
 (d) Business Expenses. The Company shall
reimburse Executive for all reasonable, documented, out-of-pocket travel and other business expenses incurred by Executive in the performance of Executive’s duties
to the Company in accordance with the Company’s applicable expense reimbursement policies and procedures as are in effect from time to time. 

(e) Vacation. Executive will be entitled to paid vacation in accordance with the Company’s vacation policy, as in effect
from time to time. 
 4. Equity Awards. Executive shall be eligible for the grant of stock options and other equity awards as may be
determined by the Board or its Compensation Committee. 
 5. Termination.

(a) At-Will Employment. The Company and Executive acknowledge that Executive’s
employment is and shall continue to be at-will, as defined under applicable law. This means that it is not for any specified period of time and, subject to any ramifications under Section 6 of this
Agreement, can be terminated by Executive or by the Company at any time, with or without advance notice, and for any or no particular reason or cause. It also means that Executive’s job duties, title, and responsibility and reporting level,
work schedule, compensation, and benefits, as well as the Company’s personnel policies and procedures, may be changed with prospective effect, with or without notice, at any time in the sole discretion of the Company (subject to any
ramification such changes may have under Section 6 of this Agreement). This “at-will” nature of Executive’s employment shall remain unchanged during Executive’s tenure as an employee
and may not be changed, except in an express writing signed by Executive and a duly-authorized officer of the Company. If Executive’s employment terminates for any lawful reason, Executive shall not be entitled to any payments, benefits,
damages, award, or compensation other than as provided in this Agreement. 
 (b) Notice of Termination. During the Term, any
termination of Executive’s employment by the Company or by Executive (other than by reason of death) shall be communicated by written notice (a “Notice of Termination”) from one Party hereto to the other Party hereto
(i) indicating the specific termination provision in this Agreement relied upon, if any, (ii) setting forth in reasonable detail the facts and circumstances claimed to provide a basis for termination of Executive’s employment under
the provision so indicated, and (iii) specifying the Date of Termination (as defined below). The failure by the Company to set forth in the Notice of Termination all of the facts and circumstances which contribute to a showing of Cause (as
defined below) shall not waive any right of the Company hereunder or preclude the Company from asserting such fact or circumstance in enforcing its rights hereunder. 

  
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 (c) Date of Termination. For purposes of this Agreement, “Date of
Termination” shall mean the date of the termination of Executive’s employment with the Company specified in a Notice of Termination. 

(d) Deemed Resignation. Upon termination of Executive’s employment for any reason, Executive shall be deemed to have
resigned from all offices and board memberships, if any, then held with the Company or any of its affiliates, and, at the Company’s request, Executive shall execute such documents as are necessary or desirable to effectuate such resignations.

 6. Consequences of Termination. 

(a) Payments of Accrued Obligations upon all Terminations of Employment. Upon a termination of Executive’s employment for
any reason, Executive (or Executive’s estate or legal representative, as applicable) shall be entitled to receive, within 30 days after Executive’s Date of Termination (or such earlier date as may be required by applicable law): (i) any
portion of Executive’s Annual Base Salary earned through Executive’s Date of Termination not theretofore paid, (ii) any expenses owed to Executive under Section 3, (iii) any accrued but unused paid time off owed to Executive,
solely to the extent applicable under the Company’s paid time off policies; (iv) any Annual Bonus earned but unpaid as of the Date of Termination, and (v) any amount arising from Executive’s participation in, or benefits under, any
employee benefit plans, programs, or arrangements under Section 3, which amounts shall be payable in accordance with the terms and conditions of such employee benefit plans, programs, or arrangements. Except as otherwise set forth in Sections
6(b) and (c), the payments and benefits described in this Section 6(a) shall be the only payments and benefits payable in the event of Executive’s termination of employment for any reason. 

(b) Severance Payments upon Covered Termination Outside a Change in Control Period. If, during the Term, Executive experiences a
Covered Termination outside of a Change in Control Period (each as defined below), then in addition to the payments and benefits described in Section 6(a), the Company shall, subject to Executive’s delivery to the Company of a waiver and
release of claims agreement in a form acceptable to the Company (the “Release”) that becomes effective and irrevocable in accordance with Section 10(d), provide Executive with the following: 

(i) Executive shall be entitled to receive an amount equal to nine (9) months of Executive’s annual base
salary at the rate in effect immediately prior to the Date of Termination, payable in a cash lump sum, less applicable withholdings, on the first payroll date following the date the Release becomes effective and irrevocable in accordance with
Section 10(d). 
 (ii) If Executive timely elects to receive continued healthcare coverage pursuant to the
provisions of the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall directly pay, or reimburse Executive for, the Company’s portion of the premium (at the same rates in
effect on the Date of Termination) for Executive and Executive’s covered dependents through the earlier of (A) the nine (9)-month anniversary of the Date of Termination and (B) the date Executive and

  
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Executive’s covered dependents, if any, become eligible for healthcare coverage under another employer’s plan(s). Notwithstanding the foregoing, (x) if any plan pursuant to which
such benefits are provided is not, or ceases prior to the expiration of the period of continuation coverage to be, exempt from the application of Section 409A of the Internal Revenue Code of 1986, as amended, (the
“Code”) under Treasury Regulation Section 1.409A-1(a)(5), or (y) the Company is otherwise unable to continue to cover Executive under its group health plans without penalty
under applicable law (including without limitation, Section 2716 of the Public Health Service Act), then, in either case, an amount equal to each remaining Company subsidy shall thereafter be paid to Executive in substantially equal monthly
installments. After the Company ceases to pay premiums pursuant to this Section 6(b)(ii), Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA. Executive shall
notify the Company immediately if Executive becomes covered by a group health plan of a subsequent employer. 
 (c) Severance
Payments upon Covered Termination During a Change in Control Period. If, during the Term, Executive experiences a Covered Termination during a Change in Control Period, then, in addition to the payments and benefits described in
Section 6(a), the Company shall, subject to Executive’s delivery to the Company of the Release that becomes effective and irrevocable in accordance with Section 10(d), provide Executive with the following: 

(i) Executive shall be entitled to receive an amount equal to the sum of (i) twelve (12) months of Executive’s
annual base salary at the rate in effect immediately prior to the Date of Termination and (ii) Executive’s target annual bonus assuming achievement of performance goals at one hundred percent (100%) of target, payable in a cash lump sum,
less applicable withholdings, on the first payroll date following the date the Release becomes effective and irrevocable in accordance with Section 10(d). 

(ii) If Executive timely elects to receive continued healthcare coverage pursuant to the provisions of COBRA, the
Company shall directly pay, or reimburse Executive for, the Company’s portion of the premium (at the same rates in effect on the Date of Termination) for Executive and Executive’s covered dependents through the earlier of (i) the
twelve (12)-month anniversary of the Date of Termination and (ii) the date Executive and Executive’s covered dependents, if any, become eligible for healthcare coverage under another employer’s plan(s). Notwithstanding the foregoing,
(i) if any plan pursuant to which such benefits are provided is not, or ceases prior to the expiration of the period of continuation coverage to be, exempt from the application of Section 409A of the Code under Treasury Regulation Section 1.409A-1(a)(5), or (ii) the Company is otherwise unable to continue to cover Executive under its group health plans without penalty under applicable law (including without limitation,
Section 2716 of the Public Health Service Act), then, in either case, an amount equal to each remaining Company subsidy shall thereafter be paid to Executive in substantially equal monthly installments. After the Company ceases to pay premiums
pursuant to this Section 6(c)(ii), Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA. Executive shall notify the Company immediately if Executive becomes
covered by a group health plan of a subsequent employer. 

  
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 (iii) Each outstanding and unvested equity award, including, without
limitation, each restricted stock, stock option, restricted stock unit and stock appreciation right, held by Executive shall automatically become vested and, if applicable, exercisable and any forfeiture restrictions or rights of repurchase thereon
shall immediately lapse with respect to one percent (100%) of the shares subject thereto, as of immediately prior to the Date of Termination. Unless otherwise set forth in an applicable award agreement, for purposes of this Section 6(c)(iii)
each award subject to performance-based vesting will be deemed earned at the greater of (A) target or (B) actual achievement measured as of the Date of Termination (to the extent then measurable). 

(d) No Other Severance. Except as otherwise approved by the Board, the provisions of this Section 6 shall supersede in their
entirety any severance payment provisions in any severance plan, policy, program, or other arrangement maintained by the Company, including without limitation, the Offer Letter. 

(e) No Requirement to Mitigate; Survival. Executive shall not be required to mitigate the amount of any payment provided for
under this Agreement by seeking other employment or in any other manner. Notwithstanding anything to the contrary in this Agreement, the termination of Executive’s employment shall not impair the rights or obligations of any Party. 

(f) Definition of Cause. For purposes hereof, “Cause” means: (i) Executive’s failure to perform
Executive’s assigned duties or responsibilities as an officer of the Company (other than a failure resulting from Executive’s Disability (as defined herein) after notice thereof from the Company describing Executive’s failure to
perform such duties or responsibilities; (ii) Executive’s engaging in any act of dishonesty, fraud or misrepresentation; (iii) Executive’s violation of any federal or state law or regulation applicable to the business of the
Company or its affiliates; (iv) Executive’s breach of any confidentiality agreement or invention assignment agreement between Executive and the Company (or any affiliate of the Company); or (v) Executive’s commission of, or
entering a plea of nolo contendere to, any crime or committing any act of moral turpitude. 
 (g) Definition of Change in
Control. For purposes hereof, “Change in Control” has the meaning ascribed to such term under the Company’s 2020 Incentive Award Plan, as may be amended from time to time; provided, that such transaction must
also constitute a “change in control event” within the meaning of Treasury Regulation Section 1.409A-3(i)(5). 

(h) Definition of Change in Control Period. For purposes hereof, “Change in Control Period” shall mean
the period commencing three months prior to a Change in Control and ending 12 months after such Change in Control. 
 (i)
Definition of Covered Termination. For purposes hereof, “Covered Termination” shall mean the termination of Executive’s employment by the Company without Cause or by Executive for Good Reason, and shall not
include a termination due to Executive’s death or disability. 

  
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 (j) Definition of Disability. For purposes hereof,
“Disability” has the meaning set forth under the long-term disability policy of the Company or a related entity to which Executive provides services regardless of whether Executive is covered by such policy. If the Company or
the related entity to which Executive provides service does not have a long-term disability plan in place, “Disability” means that Executive is unable to carry out the responsibilities and functions of the position held by Executive by
reason of any medically determinable physical or mental impairment for a period of not less than ninety (90) consecutive days. Executive will not be considered to have incurred a Disability unless Executive furnishes proof of such impairment
sufficient to satisfy the Board in its discretion. 
 (k) Definition of Good Reason. For purposes hereof, “Good
Reason” for Executive to terminate Executive’s employment hereunder shall mean the occurrence of any of the following events without Executive’s consent: (i) a material reduction in Executive’s salary or benefits
(excluding the substitution of substantially equivalent compensation and benefits), other than as a result of a reduction in compensation affecting employees of the Company, or its successor entity, generally; (ii) a material diminution in
Executive’s duties or responsibilities, provided however, that, a mere change in title or reporting relationship alone shall not constitute “Good Reason;” or (iii) relocation of Executive’s place of employment to a location
more than 50 miles from the Company’s office location, provided, in each case, that if any of the events set forth above shall occur, Executive shall give written notice of such event to the Company, or its successor entity, within thirty
(30) days following such event, and if such event is not cured within thirty (30) days from such notice (the “Cure Period”) Executive may exercise Executive’s rights to resign for Good Reason, provided that if
Executive has not exercised such right within forty-five (45) days of the expiration of the Cure Period Executive shall be deemed to have agreed to the occurrence of such event. 

7. Assignment and Successors. The Company shall assign its rights and obligations under this Agreement to any successor to all or
substantially all of the business or the assets of the Company (by merger or otherwise). This Agreement shall be binding upon and inure to the benefit of the Company, Executive, and their respective successors, assigns, personnel, and legal
representatives, executors, administrators, heirs, distributees, devisees, and legatees, as applicable. None of Executive’s rights or obligations may be assigned or transferred by Executive, other than Executive’s rights to payments
hereunder, which may be transferred only by will, operation of law, or as otherwise provided herein. 
 8. Miscellaneous Provisions.

 (a) Confidentiality Agreement. Executive hereby affirms Executive’s obligations under that certain At-Will Employment, Confidential Information, Invention Assignment, and Arbitration Agreement or other confidentiality agreement by and between the Company and Executive (the “Confidentiality
Agreement”). The Confidentiality Agreement shall survive the termination of this Agreement and Executive’s employment with the Company for the applicable period(s) set forth therein. Notwithstanding the foregoing, in the event of
any conflict between the terms of the Confidentiality Agreement and the terms of this Agreement, the terms of this Agreement shall prevail. 

(b) Governing Law. This Agreement shall be governed, construed, interpreted, and enforced in accordance with its express terms,
and otherwise in accordance with the substantive laws of the State of California, without giving effect to any principles of conflicts of law, whether of the State of California or any other jurisdiction, and where applicable, the laws of the United
States, that would result in the application of the laws of any other jurisdiction. 

  
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 (c) Validity. The invalidity or unenforceability of any provision or
provisions of this Agreement shall not affect the validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect. 

(d) Counterparts. This Agreement may be executed in several counterparts, each of which shall be deemed to be an original, but
all of which together will constitute one and the same Agreement. Signatures delivered by facsimile shall be deemed effective for all purposes. 

(e) Entire Agreement. The terms of this Agreement, together with the Confidentiality Agreement and the section entitled
“Relocation Expenses” set forth in the Offer Letter, are intended by the Parties to be the final expression of their agreement with respect to the employment of Executive by the Company and supersede all prior understandings and
agreements, whether written or oral, regarding Executive’s service to the Company, including without limitation, the Offer Letter (other than the section entitled “Relocation Expenses”). The Parties further intend that this Agreement,
together with the Confidentiality Agreement and the “Relocation Expenses” section of the Offer Letter, shall constitute the complete and exclusive statement of their terms and that no extrinsic evidence whatsoever may be introduced in any
judicial, administrative, or other legal proceeding to vary the terms of this Agreement or the Confidentiality Agreement. Notwithstanding the foregoing, in the event of any conflict between the terms of the Confidentiality Agreement and the terms of
this Agreement, the terms of this Agreement shall prevail. 
 (f) Amendments; Waivers. This Agreement may not be modified,
amended, or terminated except by an instrument in writing signed by Executive and a duly authorized representative of the Company. By an instrument in writing similarly executed, Executive or a duly authorized officer of the Company, as applicable,
may waive compliance by the other Party with any specifically identified provision of this Agreement that such other Party was or is obligated to comply with or perform; provided, however, that such waiver shall not operate as a waiver
of, or estoppel with respect to, any other or subsequent failure. No failure to exercise and no delay in exercising any right, remedy, or power hereunder shall preclude any other or further exercise of any other right, remedy, or power provided
herein or by law or in equity. 
 (g) Dispute Resolution. To ensure the timely and economical resolution of disputes that arise
in connection with this Agreement, Executive and the Company agree that, except as excluded herein, any and all controversies, claims and disputes arising out of or relating to this Agreement, including without limitation any alleged violation of
its terms or otherwise arising out of the Parties’ relationship, shall be resolved solely and exclusively by final and binding arbitration held in San Mateo County, California through JAMS in conformity with California law and the then-existing
JAMS employment arbitration rules, which can be found at https://www.jamsadr.com/rules-employment-arbitration/. The Federal Arbitration Act, 9 U.S.C. §§ 1 et seq. shall govern the interpretation and enforcement of this arbitration
clause. All remedies available from a court of competent jurisdiction shall be available in the arbitration; provided, however, in the event of a breach of Section 8(a), the Company may request relief from a court of competent jurisdiction if
such relief is not available or not available in a timely fashion through 

  
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arbitration as determined by the Company. The arbitrator shall: (a) provide adequate discovery for the resolution of the dispute; and (b) issue a written arbitration decision, to
include the arbitrator’s essential findings and conclusions and a statement of the award. The arbitrator shall award the prevailing Party attorneys’ fees and expert fees, if any. Notwithstanding the foregoing, it is acknowledged that it
will be impossible to measure in money the damages that would be suffered if the Parties fail to comply with any of the obligations imposed on them under Section 8(a), and that in the event of any such failure, an aggrieved person will be
irreparably damaged and will not have an adequate remedy at law. Any such person shall, therefore, be entitled to seek injunctive relief, including specific performance, to enforce such obligations, and if any action shall be brought in equity to
enforce any of the provisions of Section 8(a), none of the Parties shall raise the defense, without a good faith basis for raising such defense, that there is an adequate remedy at law. Executive and the Company understand that by agreement to
arbitrate any claim pursuant to this Section 8(g), they will not have the right to have any claim decided by a jury or a court, but shall instead have any claim decided through arbitration. Executive and the Company waive any constitutional or
other right to bring claims covered by this Agreement other than in their individual capacities. Except as may be prohibited by applicable law, the foregoing waiver includes the ability to assert claims as a plaintiff or class member in any
purported class or collective action or representative proceeding. Nothing herein shall limit Executive’s ability to pursue claims for workers compensation or unemployment benefits or pursue other claims which by law cannot be subject to
mandatory arbitration. 
 (h) Enforcement. If any provision of this Agreement is held to be illegal, invalid, or unenforceable
under present or future laws, such provision shall be fully severable; this Agreement shall be construed and enforced as if such illegal, invalid, or unenforceable provision had never comprised a portion of this Agreement; and the remaining
provisions of this Agreement shall remain in full force and effect and shall not be affected by the illegal, invalid, or unenforceable provision or by its severance from this Agreement. Furthermore, in lieu of such illegal, invalid, or unenforceable
provision there shall be added automatically as part of this Agreement a provision as similar in terms to such illegal, invalid, or unenforceable provision as may be possible and be legal, valid, and enforceable. 

(i) Withholding. The Company shall be entitled to withhold from any amounts payable under this Agreement any federal, state,
local, or foreign withholding or other taxes or charges which the Company is required to withhold. The Company shall be entitled to rely on an opinion of counsel if any questions as to the amount or requirement of withholding shall arise. 

(j) Whistleblower Protections and Trade Secrets. Notwithstanding anything to the contrary contained herein, nothing in this
Agreement prohibits Executive from reporting possible violations of federal law or regulation to any United States governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities
Exchange Act of 1934 or Section 806 of the Sarbanes-Oxley Act of 2002, or any other whistleblower protection provisions of state or federal law or regulation (including the right to receive an award for information provided to any such
government agencies). Furthermore, in accordance with 18 U.S.C. § 1833, notwithstanding anything to the contrary in this Agreement: (i) Executive shall not be in breach of this Agreement, and shall not be held criminally or civilly liable
under any federal or state trade secret law (x) for the disclosure of a trade secret that is made in confidence to a federal, state, or local government official or to an attorney solely for the purpose of reporting or investigating a suspected
violation of law, or (y) for the disclosure of a trade secret that is made in a complaint or other document filed in a lawsuit or other proceeding, if such filing is made under seal; and (ii) if Executive files a lawsuit for retaliation by
the Company for reporting a suspected violation of law, Executive may disclose the trade secret to Executive’s attorney, and may use the trade secret information in the court proceeding, if Executive files any document containing the trade
secret under seal, and does not disclose the trade secret, except pursuant to court order. 

  
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 9. Golden Parachute Excise Tax. 

(a) Best Pay. Any provision of this Agreement to the contrary notwithstanding, if any payment or benefit Executive would receive
from the Company pursuant to this Agreement or otherwise (“Payment”) would (i) constitute a “parachute payment” within the meaning of Section 280G of the Code and (ii) but for this sentence, be
subject to the excise tax imposed by Section 4999 of the Code (the “Excise Tax”), then such Payment will be equal to the Reduced Amount (as defined below). The “Reduced Amount” will be either
(A) the largest portion of the Payment that would result in no portion of the Payment (after reduction) being subject to the Excise Tax or (B) the entire Payment, whichever amount after taking into account all applicable federal, state,
and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate, net of the maximum reduction in federal income taxes which could be obtained from a deduction of such state and local taxes), results
in Executive’ s receipt, on an after-tax basis, of the greater economic benefit notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in a Payment is
required pursuant to the preceding sentence and the Reduced Amount is determined pursuant to clause (A) of the preceding sentence, the reduction shall occur in the manner (the “Reduction Method”) that results in the
greatest economic benefit for Executive. If more than one method of reduction will result in the same economic benefit, the items so reduced will be reduced pro rata (the “Pro Rata Reduction Method”). Notwithstanding the
foregoing, if the Reduction Method or the Pro Rata Reduction Method would result in any portion of the Payment being subject to taxes pursuant to Section 409A (as defined below) that would not otherwise be subject to taxes pursuant to
Section 409A, then the Reduction Method and/or the Pro Rata Reduction Method, as the case may be, shall be modified so as to avoid the imposition of taxes pursuant to Section 409A as follows: (1) as a first priority, the modification
shall preserve to the greatest extent possible, the greatest economic benefit for Executive as determined on an after-tax basis; (2) as a second priority, Payments that are contingent on future events
(e.g., being terminated without cause), shall be reduced (or eliminated) before Payments that are not contingent on future events; and (3) as a third priority, Payments that are “deferred compensation” within the meaning of
Section 409A shall be reduced (or eliminated) before Payments that are not deferred compensation within the meaning of Section 409A. 

(b) Accounting Firm. The accounting firm engaged by the Company for general tax purposes as of the day prior to the Change in
Control will perform the calculations set forth in Section 9(a). If the firm so engaged by the Company is serving as the accountant or auditor for the acquiring company, the Company will appoint a nationally recognized accounting firm to make
the determinations required hereunder. The Company will bear all expenses with respect to the determinations by such firm required to be made hereunder. The accounting firm engaged to make the determinations hereunder will provide its calculations,
together with detailed supporting documentation, to the Company within 30 days before the consummation of a Change in Control (if requested at that time by the Company) or such other time as requested by the Company. If the accounting firm
determines that no Excise Tax is payable with respect to a Payment, either before or after the application of the Reduced Amount, it will furnish the Company with documentation reasonably acceptable to the Company that no Excise Tax will be imposed
with respect to such Payment. Any good faith determinations of the accounting firm made hereunder will be final, binding and conclusive upon the Company and Executive. 

  
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 10. Section 409A. 

(a) General. The intent of the Parties is that the payments and benefits under this Agreement comply with or be exempt from
Section 409A of the Code and the Department of Treasury regulations and other interpretive guidance issued thereunder, including without limitation any such regulations or other guidance that may be issued after the Effective Date,
(“Section 409A”) and, accordingly, to the maximum extent permitted, this Agreement shall be interpreted to be in compliance therewith. Notwithstanding any provision of this Agreement to the
contrary, if the Company determines that any compensation or benefits payable under this Agreement may be subject to Section 409A, the Company shall work in good faith with Executive to adopt such amendments to this Agreement or adopt other
policies and procedures (including amendments, policies and procedures with retroactive effect), or take any other actions, that the Company determines are necessary or appropriate to avoid the imposition of taxes under Section 409A, including,
without limitation, actions intended to (i) exempt the compensation and benefits payable under this Agreement from Section 409A, and/or (ii) comply with the requirements of Section 409A; however, this Section 10(a) shall not
create an obligation on the part of the Company to adopt any such amendment, policy or procedure or take any such other action, nor shall the Company (A) have any liability for failing to do so, or (B) incur or indemnify Executive for any
taxes, interest or other liabilities arising under or by operation of Section 409A. 
 (b) Separation from Service,
Installments and Reimbursements. Notwithstanding any provision to the contrary in this Agreement: (i) no amount that constitutes “deferred compensation” under Section 409A shall be payable pursuant to Section 6
unless the termination of Executive’s employment constitutes a “separation from service” within the meaning of Section 1.409A-1(h) of the Department of Treasury Regulations
(“Separation from Service”); (ii) for purposes of Section 409A, Executive’s right to receive installment payments shall be treated as a right to receive a series of separate and distinct payments; and (iii) to
the extent that any reimbursement of expenses or in-kind benefits constitutes “deferred compensation” under Section 409A, such reimbursement or benefit shall be provided no later than December
31st of the year following the year in which the expense was incurred. The amount of expenses reimbursed in one year shall not affect the amount eligible for reimbursement in any subsequent year.
The amount of any in-kind benefits provided in one year shall not affect the amount of in-kind benefits provided in any other year. 

(c) Specified Employee. Notwithstanding anything in this Agreement to the contrary, if Executive is deemed by the Company at the
time of Executive’s Separation from Service to be a “specified employee” for purposes of Section 409A, to the extent delayed commencement of any portion of the benefits to which Executive is entitled under this Agreement is
required in order to avoid a prohibited distribution under Section 409A, such portion of Executive’s benefits shall not be provided to Executive prior to the earlier of (i) the expiration of the
six-month period measured from the date of Executive’s Separation from Service with the Company or (ii) the date of Executive’s death. Upon the first business day following the expiration of the
applicable Section 409A period, all payments deferred pursuant to the preceding sentence shall be paid in a lump sum to Executive (or Executive’s estate or beneficiaries), and any remaining payments due to Executive under this Agreement
shall be paid as otherwise provided herein. 

  
 11 

 (d) Release. Notwithstanding anything to the contrary in this Agreement, to
the extent that any payments due under this Agreement as a result of Executive’s termination of employment are subject to Executive’s execution and delivery of the Release, (i) if Executive fails to execute the Release on or prior to
the Release Expiration Date (as defined below) or timely revokes Executive’s acceptance of the Release thereafter, Executive shall not be entitled to any payments or benefits otherwise conditioned on the Release, and (ii) in any case where
Executive’s Date of Termination and the last day the Release may be considered or, if applicable, revoked, fall in two separate taxable years, any payments required to be made to Executive that are conditioned on the Release and are treated as
nonqualified deferred compensation for purposes of Section 409A shall be made in the later taxable year. For purposes of this Section 10(d), “Release Expiration Date” shall mean (1) if Executives is under 40
years old as of the Date of Termination, the date that is seven (7) days following the date upon which the Company timely delivers the Release to Executive, and (2) if Executive is 40 years or older as of the Date of Termination, the date
that is 21 days following the date upon which the Company timely delivers the Release to Executive, or, in the event that Executive’s termination of employment is “in connection with an exit incentive or other employment termination
program” (as such phrase is defined in the Age Discrimination in Employment Act of 1967), the date that is 45 days following such delivery date. To the extent that any payments of nonqualified deferred compensation (within the meaning of
Section 409A) due under this Agreement as a result of Executive’s termination of employment are delayed pursuant to this Section 10(d), such amounts shall be paid in a lump sum on the first payroll date following the date that
Executive executes and does not revoke the Release (and the applicable revocation period has expired) or, in the case of any payments subject to Section 10(d)(ii), on the first payroll period to occur in the subsequent taxable year, if later.

 11. Employee Acknowledgement. Executive acknowledges that Executive has read and understands this Agreement, is fully aware of its
legal effect, has not acted in reliance upon any representations or promises made by the Company other than those contained in writing herein, and has entered into this Agreement freely based on Executive’s own judgment. 

[Signature Page Follows] 

  
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 The Parties have executed this Agreement as of the date first set forth above. 

 

			
	ANNEXON, INC.
		
	By:	 	 /s/ Douglas E. Love

	Name:	 	Douglas E. Love
	Title:	 	President and Chief Executive Officer
	
	EXECUTIVE
		
	By:	 	 /s/ Sanjay Keswani

	Name:	 	Sanjay Keswani

 EXHIBIT A 

PERMITTED OUTSIDE ACTIVITIES 

1. Independent BoD Member for Proneurotech, Inc.EX-10.9

 Exhibit 10.9 

ANNEXON, INC. 

EMPLOYMENT AGREEMENT 

This Employment Agreement (the “Agreement”), is made and entered into by and between Annexon, Inc., a Delaware
corporation (the “Company”) and Jennifer Lew (“Executive” and, together with the Company, the “Parties”). This Agreement will become effective as of immediately prior to the
time the Company’s registration statement relating to the initial public offering of the Company’s common stock becomes effective (the “Effective Date”). This Agreement supersedes in its entirety that certain offer
letter between Executive and the Company dated as of April 29, 2019 (“Offer Letter”). 
 WHEREAS,
the Company desires to assure itself of the continued services of Executive by engaging Executive to perform services as an employee of the Company under the terms hereof; 

WHEREAS, Executive desires to provide continued services to the Company on the terms herein provided; and 

WHEREAS, the Parties desire to execute this Agreement to supersede the Offer Letter in its entirety and reflect certain changes to
Executive’s employment with the Company effective as of the Effective Date. 
 NOW, THEREFORE, in consideration of the
foregoing, and for other good and valuable consideration, including the respective covenants and agreements set forth below, the receipt and sufficiency of which are hereby acknowledged, the Parties hereto agree as follows: 

1. Employment. 
 (a)
General. The Company shall employ Executive upon the terms and conditions provided herein effective as of the Effective Date. 

(b) Position and Duties. Effective as of the Effective Date, Executive: (i) shall continue to serve as the Company’s
Executive Vice President and Chief Financial Officer, with responsibilities, duties, and authority usual and customary for such position, subject to direction by the Chief Executive Officer of the Company (the “CEO”); (ii)
shall continue to report directly to the CEO; and (iii) agrees promptly and faithfully to comply with all present and future policies, requirements, rules and regulations, and reasonable directions and requests, of the Company in connection
with the Company’s business. At the Company’s request, Executive shall serve the Company and/or its subsidiaries and affiliates in such other capacities in addition to the foregoing as the Company shall designate, provided that such
additional capacities are consistent with Executive’s position as the Company’s Executive Vice President and Chief Financial Officer. In the event that Executive serves in any one or more of such additional capacities, Executive’s
compensation shall not automatically be increased on account of such additional service. 

  
 1 

 (c) Principal Office. Executive shall continue to perform services for the
Company at the Company’s offices located in South San Francisco, California, or, with the Company’s consent, at any other place in connection with the fulfillment of Executive’s role with the Company; provided, however, that the
Company may from time to time require Executive to travel temporarily to other locations in connection with the Company’s business. 

(d) Exclusivity. Except with the prior written approval of the CEO (which the CEO may grant or withhold in his or her sole and
absolute discretion), Executive shall devote Executive’s best efforts and full working time, attention, and energies to the business of the Company, except during any paid vacation or other excused absence periods. Notwithstanding the
foregoing, Executive may, without violating this Section 1(d), (i) as a passive investment, own publicly traded securities in such form or manner as will not require any services by Executive in the operation of the entities in which such
securities are owned; (ii) engage in charitable and civic activities; or (iii) engage in other personal passive investment activities, in each case, so long as such interests or activities do not materially interfere to the extent such
activities do not, individually or in the aggregate, interfere with or otherwise prevent the performance of Executive’s duties and responsibilities hereunder. Executive may also serve as a member of the board of directors or board of advisors
of another organization provided (i) such organization is not a competitor of the Company; (ii) Executive receives prior written approval from the Company’s CEO; and (iii) such activities do not individually or in the aggregate
interfere with the performance of Executive’s duties under this Agreement, violate the Company’s standards of conduct then in effect, or raise a conflict under the Company’s conflict of interest policies. For the avoidance of doubt,
the CEO has approved Executive’s continued service with those organizations set forth on Exhibit A, such approval to continue until the earlier to occur of (a) the CEO’s revocation of such approval in his or her sole and
absolute discretion, or (b) such time as such service interferes with the performance of Executive’s duties under this Agreement, violates the Company’s standards of conflict or raises a conflict under the Company’s conflict of
interest policies. 
 2. Term. The period of Executive’s employment under this Agreement shall commence on the Effective Date and
shall continue until Executive’s employment with the Company is terminated pursuant to Section 5. The phrase “Term” as used in this Agreement shall refer to the entire period of employment of Executive by the
Company. 
 3. Compensation and Related Matters. 

(a) Annual Base Salary. During the Term, Executive shall receive a base salary at the rate of $371,900 per year (as may be
increased from time to time, the “Annual Base Salary”), subject to withholdings and deductions, which shall be paid to Executive in accordance with the customary payroll practices and procedures of the Company. Such Annual
Base Salary shall be reviewed by the CEO, and, as applicable, the Board of Directors of the Company (the “Board”) and/or the Compensation Committee of the Board, not less than annually. 

(b) Annual Bonus. Executive shall be eligible to receive a discretionary annual bonus based on Executive’s achievement of
performance objectives established by the Board, its Compensation Committee and/or the CEO, such bonus to be targeted at 40% of Executive’s Annual Base Salary (the “Annual Bonus”). Any Annual Bonus approved by the Board
or the Compensation Committee of the Board shall be paid at the same time annual bonuses are paid to other executives of the Company generally, subject to Executive’s continuous employment through the date of approval. 

  
 2 

 (c) Benefits. Executive shall be entitled to participate in such employee and
executive benefit plans and programs as the Company may from time to time offer to provide to its executives, subject to the terms and conditions of such plans. Notwithstanding the foregoing, nothing herein is intended, or shall be construed, to
require the Company to institute or continue any particular plan or benefit. 
 (d) Business Expenses. The Company shall
reimburse Executive for all reasonable, documented, out-of-pocket travel and other business expenses incurred by Executive in the performance of Executive’s duties
to the Company in accordance with the Company’s applicable expense reimbursement policies and procedures as are in effect from time to time. 

(e) Vacation. Executive will be entitled to paid vacation in accordance with the Company’s vacation policy, as in effect
from time to time. 
 4. Equity Awards. Executive shall be eligible for the grant of stock options and other equity awards as may be
determined by the Board or its Compensation Committee. 
 5. Termination.

(a) At-Will Employment. The Company and Executive acknowledge that Executive’s
employment is and shall continue to be at-will, as defined under applicable law. This means that it is not for any specified period of time and, subject to any ramifications under Section 6 of this
Agreement, can be terminated by Executive or by the Company at any time, with or without advance notice, and for any or no particular reason or cause. It also means that Executive’s job duties, title, and responsibility and reporting level,
work schedule, compensation, and benefits, as well as the Company’s personnel policies and procedures, may be changed with prospective effect, with or without notice, at any time in the sole discretion of the Company (subject to any
ramification such changes may have under Section 6 of this Agreement). This “at-will” nature of Executive’s employment shall remain unchanged during Executive’s tenure as an employee
and may not be changed, except in an express writing signed by Executive and a duly-authorized officer of the Company. If Executive’s employment terminates for any lawful reason, Executive shall not be entitled to any payments, benefits,
damages, award, or compensation other than as provided in this Agreement. 
 (b) Notice of Termination. During the Term, any
termination of Executive’s employment by the Company or by Executive (other than by reason of death) shall be communicated by written notice (a “Notice of Termination”) from one Party hereto to the other Party hereto
(i) indicating the specific termination provision in this Agreement relied upon, if any, (ii) setting forth in reasonable detail the facts and circumstances claimed to provide a basis for termination of Executive’s employment under
the provision so indicated, and (iii) specifying the Date of Termination (as defined below). The failure by the Company to set forth in the Notice of Termination all of the facts and circumstances which contribute to a showing of Cause (as
defined below) shall not waive any right of the Company hereunder or preclude the Company from asserting such fact or circumstance in enforcing its rights hereunder. 

  
 3 

 (c) Date of Termination. For purposes of this Agreement, “Date of
Termination” shall mean the date of the termination of Executive’s employment with the Company specified in a Notice of Termination. 

(d) Deemed Resignation. Upon termination of Executive’s employment for any reason, Executive shall be deemed to have
resigned from all offices and board memberships, if any, then held with the Company or any of its affiliates, and, at the Company’s request, Executive shall execute such documents as are necessary or desirable to effectuate such resignations.

 6. Consequences of Termination. 

(a) Payments of Accrued Obligations upon all Terminations of Employment. Upon a termination of Executive’s employment for
any reason, Executive (or Executive’s estate or legal representative, as applicable) shall be entitled to receive, within 30 days after Executive’s Date of Termination (or such earlier date as may be required by applicable law): (i) any
portion of Executive’s Annual Base Salary earned through Executive’s Date of Termination not theretofore paid, (ii) any expenses owed to Executive under Section 3, (iii) any accrued but unused paid time off owed to Executive,
solely to the extent applicable under the Company’s paid time off policies; (iv) any Annual Bonus earned but unpaid as of the Date of Termination, and (v) any amount arising from Executive’s participation in, or benefits under, any
employee benefit plans, programs, or arrangements under Section 3, which amounts shall be payable in accordance with the terms and conditions of such employee benefit plans, programs, or arrangements. Except as otherwise set forth in Sections
6(b) and (c), the payments and benefits described in this Section 6(a) shall be the only payments and benefits payable in the event of Executive’s termination of employment for any reason. 

(b) Severance Payments upon Covered Termination Outside a Change in Control Period. If, during the Term, Executive experiences a
Covered Termination outside of a Change in Control Period (each as defined below), then in addition to the payments and benefits described in Section 6(a), the Company shall, subject to Executive’s delivery to the Company of a waiver and
release of claims agreement in a form acceptable to the Company (the “Release”) that becomes effective and irrevocable in accordance with Section 10(d), provide Executive with the following: 

(i) Executive shall be entitled to receive an amount equal to nine (9) months of Executive’s annual base
salary at the rate in effect immediately prior to the Date of Termination, payable in a cash lump sum, less applicable withholdings, on the first payroll date following the date the Release becomes effective and irrevocable in accordance with
Section 10(d). 
 (ii) If Executive timely elects to receive continued healthcare coverage pursuant to the
provisions of the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall directly pay, or reimburse Executive for, the Company’s portion of the premium (at the same rates in
effect on the Date of Termination) for Executive and Executive’s covered dependents through the earlier of (A) the nine (9)-month anniversary of the Date of Termination and (B) the date Executive and

  
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Executive’s covered dependents, if any, become eligible for healthcare coverage under another employer’s plan(s). Notwithstanding the foregoing, (x) if any plan pursuant to which
such benefits are provided is not, or ceases prior to the expiration of the period of continuation coverage to be, exempt from the application of Section 409A of the Internal Revenue Code of 1986, as amended, (the
“Code”) under Treasury Regulation Section 1.409A-1(a)(5), or (y) the Company is otherwise unable to continue to cover Executive under its group health plans without penalty
under applicable law (including without limitation, Section 2716 of the Public Health Service Act), then, in either case, an amount equal to each remaining Company subsidy shall thereafter be paid to Executive in substantially equal monthly
installments. After the Company ceases to pay premiums pursuant to this Section 6(b)(ii), Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA. Executive shall
notify the Company immediately if Executive becomes covered by a group health plan of a subsequent employer. 
 (c) Severance
Payments upon Covered Termination During a Change in Control Period. If, during the Term, Executive experiences a Covered Termination during a Change in Control Period, then, in addition to the payments and benefits described in
Section 6(a), the Company shall, subject to Executive’s delivery to the Company of the Release that becomes effective and irrevocable in accordance with Section 10(d), provide Executive with the following: 

(i) Executive shall be entitled to receive an amount equal to the sum of (i) twelve (12) months of Executive’s
annual base salary at the rate in effect immediately prior to the Date of Termination and (ii) Executive’s target annual bonus assuming achievement of performance goals at one hundred percent (100%) of target, payable in a cash lump sum,
less applicable withholdings, on the first payroll date following the date the Release becomes effective and irrevocable in accordance with Section 10(d). 

(ii) If Executive timely elects to receive continued healthcare coverage pursuant to the provisions of COBRA, the
Company shall directly pay, or reimburse Executive for, the Company’s portion of the premium (at the same rates in effect on the Date of Termination) for Executive and Executive’s covered dependents through the earlier of (i) the
twelve (12)-month anniversary of the Date of Termination and (ii) the date Executive and Executive’s covered dependents, if any, become eligible for healthcare coverage under another employer’s plan(s). Notwithstanding the foregoing,
(i) if any plan pursuant to which such benefits are provided is not, or ceases prior to the expiration of the period of continuation coverage to be, exempt from the application of Section 409A of the Code under Treasury Regulation Section 1.409A-1(a)(5), or (ii) the Company is otherwise unable to continue to cover Executive under its group health plans without penalty under applicable law (including without limitation,
Section 2716 of the Public Health Service Act), then, in either case, an amount equal to each remaining Company subsidy shall thereafter be paid to Executive in substantially equal monthly installments. After the Company ceases to pay premiums
pursuant to this Section 6(c)(ii), Executive may, if eligible, elect to continue healthcare coverage at Executive’s expense in accordance with the provisions of COBRA. Executive shall notify the Company immediately if Executive becomes
covered by a group health plan of a subsequent employer. 

  
 5 

 (iii) Each outstanding and unvested equity award, including, without
limitation, each restricted stock, stock option, restricted stock unit and stock appreciation right, held by Executive shall automatically become vested and, if applicable, exercisable and any forfeiture restrictions or rights of repurchase thereon
shall immediately lapse with respect to one percent (100%) of the shares subject thereto, as of immediately prior to the Date of Termination. Unless otherwise set forth in an applicable award agreement, for purposes of this Section 6(c)(iii)
each award subject to performance-based vesting will be deemed earned at the greater of (A) target or (B) actual achievement measured as of the Date of Termination (to the extent then measurable). 

(d) No Other Severance. Except as otherwise approved by the Board, the provisions of this Section 6 shall supersede in their
entirety any severance payment provisions in any severance plan, policy, program, or other arrangement maintained by the Company, including without limitation, the Offer Letter. 

(e) No Requirement to Mitigate; Survival. Executive shall not be required to mitigate the amount of any payment provided for
under this Agreement by seeking other employment or in any other manner. Notwithstanding anything to the contrary in this Agreement, the termination of Executive’s employment shall not impair the rights or obligations of any Party. 

(f) Definition of Cause. For purposes hereof, “Cause” means: (i) Executive’s failure to perform
Executive’s assigned duties or responsibilities as an officer of the Company (other than a failure resulting from Executive’s Disability (as defined herein) after notice thereof from the Company describing Executive’s failure to
perform such duties or responsibilities; (ii) Executive’s engaging in any act of dishonesty, fraud or misrepresentation; (iii) Executive’s violation of any federal or state law or regulation applicable to the business of the
Company or its affiliates; (iv) Executive’s breach of any confidentiality agreement or invention assignment agreement between Executive and the Company (or any affiliate of the Company); or (v) Executive’s commission of, or
entering a plea of nolo contendere to, any crime or committing any act of moral turpitude. 
 (g) Definition of Change in
Control. For purposes hereof, “Change in Control” has the meaning ascribed to such term under the Company’s 2020 Incentive Award Plan, as may be amended from time to time; provided, that such transaction must
also constitute a “change in control event” within the meaning of Treasury Regulation Section 1.409A-3(i)(5). 

(h) Definition of Change in Control Period. For purposes hereof, “Change in Control Period” shall mean
the period commencing three months prior to a Change in Control and ending 12 months after such Change in Control. 
 (i)
Definition of Covered Termination. For purposes hereof, “Covered Termination” shall mean the termination of Executive’s employment by the Company without Cause or by Executive for Good Reason, and shall not
include a termination due to Executive’s death or disability. 

  
 6 

 (j) Definition of Disability. For purposes hereof,
“Disability” has the meaning set forth under the long-term disability policy of the Company or a related entity to which Executive provides services regardless of whether Executive is covered by such policy. If the Company or
the related entity to which Executive provides service does not have a long-term disability plan in place, “Disability” means that Executive is unable to carry out the responsibilities and functions of the position held by Executive by
reason of any medically determinable physical or mental impairment for a period of not less than ninety (90) consecutive days. Executive will not be considered to have incurred a Disability unless Executive furnishes proof of such impairment
sufficient to satisfy the Board in its discretion. 
 (k) Definition of Good Reason. For purposes hereof, “Good
Reason” for Executive to terminate Executive’s employment hereunder shall mean the occurrence of any of the following events without Executive’s consent: (i) a material reduction in Executive’s salary or benefits
(excluding the substitution of substantially equivalent compensation and benefits), other than as a result of a reduction in compensation affecting employees of the Company, or its successor entity, generally; (ii) a material diminution in
Executive’s duties or responsibilities, provided however, that, a mere change in title or reporting relationship alone shall not constitute “Good Reason;” or (iii) relocation of Executive’s place of employment to a location
more than 50 miles from the Company’s office location, provided, in each case, that if any of the events set forth above shall occur, Executive shall give written notice of such event to the Company, or its successor entity, within thirty
(30) days following such event, and if such event is not cured within thirty (30) days from such notice (the “Cure Period”) Executive may exercise Executive’s rights to resign for Good Reason, provided that if
Executive has not exercised such right within forty-five (45) days of the expiration of the Cure Period Executive shall be deemed to have agreed to the occurrence of such event. 

7. Assignment and Successors. The Company shall assign its rights and obligations under this Agreement to any successor to all or
substantially all of the business or the assets of the Company (by merger or otherwise). This Agreement shall be binding upon and inure to the benefit of the Company, Executive, and their respective successors, assigns, personnel, and legal
representatives, executors, administrators, heirs, distributees, devisees, and legatees, as applicable. None of Executive’s rights or obligations may be assigned or transferred by Executive, other than Executive’s rights to payments
hereunder, which may be transferred only by will, operation of law, or as otherwise provided herein. 
 8. Miscellaneous Provisions.

 (a) Confidentiality Agreement. Executive hereby affirms Executive’s obligations under that certain At-Will Employment, Confidential Information, Invention Assignment, and Arbitration Agreement or other confidentiality agreement by and between the Company and Executive (the “Confidentiality
Agreement”). The Confidentiality Agreement shall survive the termination of this Agreement and Executive’s employment with the Company for the applicable period(s) set forth therein. Notwithstanding the foregoing, in the event of
any conflict between the terms of the Confidentiality Agreement and the terms of this Agreement, the terms of this Agreement shall prevail. 

(b) Governing Law. This Agreement shall be governed, construed, interpreted, and enforced in accordance with its express terms,
and otherwise in accordance with the substantive laws of the State of California, without giving effect to any principles of conflicts of law, whether of the State of California or any other jurisdiction, and where applicable, the laws of the United
States, that would result in the application of the laws of any other jurisdiction. 

  
 7 

 (c) Validity. The invalidity or unenforceability of any provision or
provisions of this Agreement shall not affect the validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect. 

(d) Counterparts. This Agreement may be executed in several counterparts, each of which shall be deemed to be an original, but
all of which together will constitute one and the same Agreement. Signatures delivered by facsimile shall be deemed effective for all purposes. 

(e) Entire Agreement. The terms of this Agreement, together with the Confidentiality Agreement, are intended by the Parties to be
the final expression of their agreement with respect to the employment of Executive by the Company and supersede all prior understandings and agreements, whether written or oral, regarding Executive’s service to the Company, including without
limitation, the Offer Letter. The Parties further intend that this Agreement, together with the Confidentiality Agreement, shall constitute the complete and exclusive statement of their terms and that no extrinsic evidence whatsoever may be
introduced in any judicial, administrative, or other legal proceeding to vary the terms of this Agreement or the Confidentiality Agreement. Notwithstanding the foregoing, in the event of any conflict between the terms of the Confidentiality
Agreement and the terms of this Agreement, the terms of this Agreement shall prevail. 
 (f) Amendments; Waivers. This
Agreement may not be modified, amended, or terminated except by an instrument in writing signed by Executive and a duly authorized representative of the Company. By an instrument in writing similarly executed, Executive or a duly authorized officer
of the Company, as applicable, may waive compliance by the other Party with any specifically identified provision of this Agreement that such other Party was or is obligated to comply with or perform; provided, however, that such
waiver shall not operate as a waiver of, or estoppel with respect to, any other or subsequent failure. No failure to exercise and no delay in exercising any right, remedy, or power hereunder shall preclude any other or further exercise of any other
right, remedy, or power provided herein or by law or in equity. 
 (g) Dispute Resolution. To ensure the timely and economical
resolution of disputes that arise in connection with this Agreement, Executive and the Company agree that, except as excluded herein, any and all controversies, claims and disputes arising out of or relating to this Agreement, including without
limitation any alleged violation of its terms or otherwise arising out of the Parties’ relationship, shall be resolved solely and exclusively by final and binding arbitration held in San Mateo County, California through JAMS in conformity with
California law and the then-existing JAMS employment arbitration rules, which can be found at https://www.jamsadr.com/rules-employment-arbitration/. The Federal Arbitration Act, 9 U.S.C. §§ 1 et seq. shall govern the interpretation
and enforcement of this arbitration clause. All remedies available from a court of competent jurisdiction shall be available in the arbitration; provided, however, in the event of a breach of Section 8(a), the Company may request relief from a
court of competent jurisdiction if such relief is not available or not available in a timely fashion through arbitration as determined by the Company. The arbitrator shall: (a) provide adequate discovery for the resolution of the dispute; and
(b) issue a written arbitration decision, to include the arbitrator’s 

  
 8 

 
essential findings and conclusions and a statement of the award. The arbitrator shall award the prevailing Party attorneys’ fees and expert fees, if any. Notwithstanding the foregoing, it is
acknowledged that it will be impossible to measure in money the damages that would be suffered if the Parties fail to comply with any of the obligations imposed on them under Section 8(a), and that in the event of any such failure, an aggrieved
person will be irreparably damaged and will not have an adequate remedy at law. Any such person shall, therefore, be entitled to seek injunctive relief, including specific performance, to enforce such obligations, and if any action shall be brought
in equity to enforce any of the provisions of Section 8(a), none of the Parties shall raise the defense, without a good faith basis for raising such defense, that there is an adequate remedy at law. Executive and the Company understand that by
agreement to arbitrate any claim pursuant to this Section 8(g), they will not have the right to have any claim decided by a jury or a court, but shall instead have any claim decided through arbitration. Executive and the Company waive any
constitutional or other right to bring claims covered by this Agreement other than in their individual capacities. Except as may be prohibited by applicable law, the foregoing waiver includes the ability to assert claims as a plaintiff or class
member in any purported class or collective action or representative proceeding. Nothing herein shall limit Executive’s ability to pursue claims for workers compensation or unemployment benefits or pursue other claims which by law cannot be
subject to mandatory arbitration. 
 (h) Enforcement. If any provision of this Agreement is held to be illegal, invalid, or
unenforceable under present or future laws, such provision shall be fully severable; this Agreement shall be construed and enforced as if such illegal, invalid, or unenforceable provision had never comprised a portion of this Agreement; and the
remaining provisions of this Agreement shall remain in full force and effect and shall not be affected by the illegal, invalid, or unenforceable provision or by its severance from this Agreement. Furthermore, in lieu of such illegal, invalid, or
unenforceable provision there shall be added automatically as part of this Agreement a provision as similar in terms to such illegal, invalid, or unenforceable provision as may be possible and be legal, valid, and enforceable. 

(i) Withholding. The Company shall be entitled to withhold from any amounts payable under this Agreement any federal, state,
local, or foreign withholding or other taxes or charges which the Company is required to withhold. The Company shall be entitled to rely on an opinion of counsel if any questions as to the amount or requirement of withholding shall arise. 

(j) Whistleblower Protections and Trade Secrets. Notwithstanding anything to the contrary contained herein, nothing in this
Agreement prohibits Executive from reporting possible violations of federal law or regulation to any United States governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities
Exchange Act of 1934 or Section 806 of the Sarbanes-Oxley Act of 2002, or any other whistleblower protection provisions of state or federal law or regulation (including the right to receive an award for information provided to any such
government agencies). Furthermore, in accordance with 18 U.S.C. § 1833, notwithstanding anything to the contrary in this Agreement: (i) Executive shall not be in breach of this Agreement, and shall not be held criminally or civilly liable
under any federal or state trade secret law (x) for the disclosure of a trade secret that is made in confidence to a federal, state, or local government official or to an attorney solely for the purpose of reporting or investigating a suspected
violation of law, or (y) for the disclosure of a trade secret that is made in a complaint or other document filed in a lawsuit or other proceeding, if such filing is made under seal; and (ii) if Executive files a lawsuit for retaliation by
the Company for reporting a suspected violation of law, Executive may disclose the trade secret to Executive’s attorney, and may use the trade secret information in the court proceeding, if Executive files any document containing the trade
secret under seal, and does not disclose the trade secret, except pursuant to court order. 

  
 9 

 9. Golden Parachute Excise Tax. 

(a) Best Pay. Any provision of this Agreement to the contrary notwithstanding, if any payment or benefit Executive would receive
from the Company pursuant to this Agreement or otherwise (“Payment”) would (i) constitute a “parachute payment” within the meaning of Section 280G of the Code and (ii) but for this sentence, be
subject to the excise tax imposed by Section 4999 of the Code (the “Excise Tax”), then such Payment will be equal to the Reduced Amount (as defined below). The “Reduced Amount” will be either
(A) the largest portion of the Payment that would result in no portion of the Payment (after reduction) being subject to the Excise Tax or (B) the entire Payment, whichever amount after taking into account all applicable federal, state,
and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate, net of the maximum reduction in federal income taxes which could be obtained from a deduction of such state and local taxes), results
in Executive’ s receipt, on an after-tax basis, of the greater economic benefit notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in a Payment is
required pursuant to the preceding sentence and the Reduced Amount is determined pursuant to clause (A) of the preceding sentence, the reduction shall occur in the manner (the “Reduction Method”) that results in the
greatest economic benefit for Executive. If more than one method of reduction will result in the same economic benefit, the items so reduced will be reduced pro rata (the “Pro Rata Reduction Method”). Notwithstanding the
foregoing, if the Reduction Method or the Pro Rata Reduction Method would result in any portion of the Payment being subject to taxes pursuant to Section 409A (as defined below) that would not otherwise be subject to taxes pursuant to
Section 409A, then the Reduction Method and/or the Pro Rata Reduction Method, as the case may be, shall be modified so as to avoid the imposition of taxes pursuant to Section 409A as follows: (1) as a first priority, the modification
shall preserve to the greatest extent possible, the greatest economic benefit for Executive as determined on an after-tax basis; (2) as a second priority, Payments that are contingent on future events
(e.g., being terminated without cause), shall be reduced (or eliminated) before Payments that are not contingent on future events; and (3) as a third priority, Payments that are “deferred compensation” within the meaning of
Section 409A shall be reduced (or eliminated) before Payments that are not deferred compensation within the meaning of Section 409A. 

(b) Accounting Firm. The accounting firm engaged by the Company for general tax purposes as of the day prior to the Change in
Control will perform the calculations set forth in Section 9(a). If the firm so engaged by the Company is serving as the accountant or auditor for the acquiring company, the Company will appoint a nationally recognized accounting firm to make
the determinations required hereunder. The Company will bear all expenses with respect to the determinations by such firm required to be made hereunder. The accounting firm engaged to make the determinations hereunder will provide its calculations,
together with detailed supporting documentation, to the Company within 30 days before the consummation of a Change in Control (if requested at that time by the Company) or such other time as requested by the Company. If the accounting firm
determines that no Excise Tax is payable with respect to a Payment, either before or after the application of the Reduced Amount, it will furnish the Company with documentation reasonably acceptable to the Company that no Excise Tax will be imposed
with respect to such Payment. Any good faith determinations of the accounting firm made hereunder will be final, binding and conclusive upon the Company and Executive. 

  
 10 

 10. Section 409A. 

(a) General. The intent of the Parties is that the payments and benefits under this Agreement comply with or be exempt from
Section 409A of the Code and the Department of Treasury regulations and other interpretive guidance issued thereunder, including without limitation any such regulations or other guidance that may be issued after the Effective Date,
(“Section 409A”) and, accordingly, to the maximum extent permitted, this Agreement shall be interpreted to be in compliance therewith. Notwithstanding any provision of this Agreement to the
contrary, if the Company determines that any compensation or benefits payable under this Agreement may be subject to Section 409A, the Company shall work in good faith with Executive to adopt such amendments to this Agreement or adopt other
policies and procedures (including amendments, policies and procedures with retroactive effect), or take any other actions, that the Company determines are necessary or appropriate to avoid the imposition of taxes under Section 409A, including,
without limitation, actions intended to (i) exempt the compensation and benefits payable under this Agreement from Section 409A, and/or (ii) comply with the requirements of Section 409A; however, this Section 10(a) shall not
create an obligation on the part of the Company to adopt any such amendment, policy or procedure or take any such other action, nor shall the Company (A) have any liability for failing to do so, or (B) incur or indemnify Executive for any
taxes, interest or other liabilities arising under or by operation of Section 409A. 
 (b) Separation from Service,
Installments and Reimbursements. Notwithstanding any provision to the contrary in this Agreement: (i) no amount that constitutes “deferred compensation” under Section 409A shall be payable pursuant to Section 6
unless the termination of Executive’s employment constitutes a “separation from service” within the meaning of Section 1.409A-1(h) of the Department of Treasury Regulations
(“Separation from Service”); (ii) for purposes of Section 409A, Executive’s right to receive installment payments shall be treated as a right to receive a series of separate and distinct payments; and (iii) to
the extent that any reimbursement of expenses or in-kind benefits constitutes “deferred compensation” under Section 409A, such reimbursement or benefit shall be provided no later than December
31st of the year following the year in which the expense was incurred. The amount of expenses reimbursed in one year shall not affect the amount eligible for reimbursement in any subsequent year.
The amount of any in-kind benefits provided in one year shall not affect the amount of in-kind benefits provided in any other year. 

(c) Specified Employee. Notwithstanding anything in this Agreement to the contrary, if Executive is deemed by the Company at the
time of Executive’s Separation from Service to be a “specified employee” for purposes of Section 409A, to the extent delayed commencement of any portion of the benefits to which Executive is entitled under this Agreement is
required in order to avoid a prohibited distribution under Section 409A, such portion of Executive’s benefits shall not be provided to Executive prior to the earlier of (i) the expiration of the
six-month period measured from the date of Executive’s Separation from Service with the Company or (ii) the date of Executive’s death. Upon the first business day following the expiration of the
applicable Section 409A period, all payments deferred pursuant to the preceding sentence shall be paid in a lump sum to Executive (or Executive’s estate or beneficiaries), and any remaining payments due to Executive under this Agreement
shall be paid as otherwise provided herein. 

  
 11 

 (d) Release. Notwithstanding anything to the contrary in this Agreement, to
the extent that any payments due under this Agreement as a result of Executive’s termination of employment are subject to Executive’s execution and delivery of the Release, (i) if Executive fails to execute the Release on or prior to
the Release Expiration Date (as defined below) or timely revokes Executive’s acceptance of the Release thereafter, Executive shall not be entitled to any payments or benefits otherwise conditioned on the Release, and (ii) in any case where
Executive’s Date of Termination and the last day the Release may be considered or, if applicable, revoked, fall in two separate taxable years, any payments required to be made to Executive that are conditioned on the Release and are treated as
nonqualified deferred compensation for purposes of Section 409A shall be made in the later taxable year. For purposes of this Section 10(d), “Release Expiration Date” shall mean (1) if Executives is under 40
years old as of the Date of Termination, the date that is seven (7) days following the date upon which the Company timely delivers the Release to Executive, and (2) if Executive is 40 years or older as of the Date of Termination, the date
that is 21 days following the date upon which the Company timely delivers the Release to Executive, or, in the event that Executive’s termination of employment is “in connection with an exit incentive or other employment termination
program” (as such phrase is defined in the Age Discrimination in Employment Act of 1967), the date that is 45 days following such delivery date. To the extent that any payments of nonqualified deferred compensation (within the meaning of
Section 409A) due under this Agreement as a result of Executive’s termination of employment are delayed pursuant to this Section 10(d), such amounts shall be paid in a lump sum on the first payroll date following the date that
Executive executes and does not revoke the Release (and the applicable revocation period has expired) or, in the case of any payments subject to Section 10(d)(ii), on the first payroll period to occur in the subsequent taxable year, if later.

 11. Employee Acknowledgement. Executive acknowledges that Executive has read and understands this Agreement, is fully aware of its legal effect,
has not acted in reliance upon any representations or promises made by the Company other than those contained in writing herein, and has entered into this Agreement freely based on Executive’s own judgment. 

[Signature Page Follows] 

  
 12 

 The Parties have executed this Agreement as of the date first set forth above. 

 

			
	ANNEXON, INC.
		
	By:	 	 /s/ Douglas E. Love

	Name:	 	Douglas E. Love
	Title:	 	President and Chief Executive Officer
	
	EXECUTIVE
		
	By:	 	 /s/ Jennifer Lew

 
			
	Name:	 	Jennifer Lew

 EXHIBIT A 

PERMITTED OUTSIDE ACTIVITIES 

1. None.

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