Document:

EX-10.3

 Exhibit 10.3 

CODIAK BIOSCIENCES, INC. 

2020 EMPLOYEE STOCK PURCHASE PLAN 

The purpose of the Codiak BioSciences, Inc. 2020 Employee Stock Purchase Plan (the “Plan”) is to provide eligible employees
of Codiak BioSciences, Inc. (the “Company”) and each Designated Subsidiary (as defined in Section 11) with opportunities to purchase shares of the Company’s common stock, par value $0.0001 per share (the “Common
Stock”). 208,680 shares of Common Stock in the aggregate have been approved and reserved for this purpose, plus on January 1, 2021, and each January 1 thereafter through January 1, 2030, the number of shares of Common Stock
reserved and available for issuance under the Plan shall be cumulatively increased by the least of (i) 834,720 shares of Common Stock, (ii) one-half percent (0.5%) of the number of shares of Common Stock
issued and outstanding on the immediately preceding December 31st, or (ii) such lesser number of shares of Common Stock as determined by the Administrator. The Plan is intended to constitute an “employee stock purchase plan” within
the meaning of Section 423(b) of the Internal Revenue Code of 1986, as amended (the “Code”), and shall be interpreted in accordance with that intent. 

1.    Administration. The Plan will be administered by the person or persons (the “Administrator”)
appointed by the Company’s Board of Directors (the “Board”) for such purpose. The Administrator has authority at any time to: (i) adopt, alter and repeal such rules, guidelines and practices for the administration of the
Plan and for its own acts and proceedings as it shall deem advisable; (ii) interpret the terms and provisions of the Plan; (iii) make all determinations it deems advisable for the administration of the Plan; (iv) decide all disputes
arising in connection with the Plan; and (v) otherwise supervise the administration of the Plan. All interpretations and decisions of the Administrator shall be binding on all persons, including

 
the Company and the Participants. No member of the Board or individual exercising administrative authority with respect to the Plan shall be liable for any action or determination made in good
faith with respect to the Plan or any option granted hereunder. 
 2.    Offerings. The Company will make one or
more offerings to eligible employees to purchase Common Stock under the Plan (“Offerings”). Unless otherwise determined by the Administrator, an Offering will begin on the first business day occurring on or after each January 1
and July 1 and will end on the last business day occurring on or before the following June 30 and December 31, respectively. The Administrator may, in its discretion, designate a different period for any Offering, provided that no
Offering shall exceed 27 months in duration or overlap any other Offering. 
 3.    Eligibility. All individuals
classified as employees on the payroll records of the Company and each Designated Subsidiary are eligible to participate in any one or more of the Offerings under the Plan, provided that as of the first day of the applicable Offering (the
“Offering Date”) they are customarily employed by the Company or a Designated Subsidiary for more than 20 hours a week. Notwithstanding any other provision herein, individuals who are not contemporaneously classified as employees of
the Company or a Designated Subsidiary for purposes of the Company’s or applicable Designated Subsidiary’s payroll system are not considered to be eligible employees of the Company or any Designated Subsidiary and shall not be eligible to
participate in the Plan. In the event any such individuals are reclassified as employees of the Company or a Designated Subsidiary for any purpose, including, without limitation, common law or statutory employees, by any action of any third party,
including, without limitation, any government agency, or as a result of any private lawsuit, action or administrative proceeding, such individuals shall, notwithstanding such reclassification, remain

  
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ineligible for participation. Notwithstanding the foregoing, the exclusive means for individuals who are not contemporaneously classified as employees of the Company or a Designated Subsidiary on
the Company’s or Designated Subsidiary’s payroll system to become eligible to participate in this Plan is through an amendment to this Plan, duly executed by the Company, which specifically renders such individuals eligible to participate
herein. 
 4.    Participation. 

(a)    Participants in Subsequent Offerings. An eligible employee who is not a Participant in any prior Offering
may participate in a subsequent Offering by submitting an enrollment form to his or her appropriate payroll location at least 15 business days before the Offering Date (or by such other deadline as shall be established by the Administrator for the
Offering). 
 (b)    Enrollment. The enrollment form will (a) state a whole percentage or the amount to be
deducted from an eligible employee’s Compensation (as defined in Section 11) per pay period, (b) authorize the purchase of Common Stock in each Offering in accordance with the terms of the Plan and (c) specify the exact name or
names in which shares of Common Stock purchased for such individual are to be issued pursuant to Section 10. An employee who does not enroll in accordance with these procedures will be deemed to have waived the right to participate. Unless a
Participant files a new enrollment form or withdraws from the Plan, such Participant’s deductions and purchases will continue at the same percentage or amount of Compensation for future Offerings, provided he or she remains eligible. 

(c)    Notwithstanding the foregoing, participation in the Plan will neither be permitted nor be denied contrary to the
requirements of the Code. 

  
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 5.    Employee Contributions. Each eligible employee may
authorize payroll deductions at a minimum of 1 percent up to a maximum of 15 percent of such employee’s Compensation for each pay period. The Company will maintain book accounts showing the amount of payroll deductions made by each
Participant for each Offering. No interest will accrue or be paid on payroll deductions. 
 6.    Deduction
Changes. Except as may be determined by the Administrator in advance of an Offering, a Participant may not increase or decrease his or her payroll deduction during any Offering, but may increase or decrease his or her payroll deduction with
respect to the next Offering (subject to the limitations of Section 5) by filing a new enrollment form at least 15 business days before the next Offering Date (or by such other deadline as shall be established by the Administrator for the
Offering). The Administrator may, in advance of any Offering, establish rules permitting a Participant to increase, decrease or terminate his or her payroll deduction during an Offering. 

7.    Withdrawal. A Participant may withdraw from participation in the Plan by delivering a written notice of
withdrawal to his or her appropriate payroll location. The Participant’s withdrawal will be effective as of the next business day. Following a Participant’s withdrawal, the Company will promptly refund such individual’s entire account
balance under the Plan to him or her (after payment for any Common Stock purchased before the effective date of withdrawal). Partial withdrawals are not permitted. Such an employee may not begin participation again during the remainder of the
Offering, but may enroll in a subsequent Offering in accordance with Section 4. 
 8.    Grant of Options.
On each Offering Date, the Company will grant to each eligible employee who is then a Participant in the Plan an option (“Option”) to purchase on the last day 

  
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of such Offering (the “Exercise Date”), at the Option Price hereinafter provided for, the lowest of (a) a number of shares of Common Stock determined by dividing such
Participant’s accumulated payroll deductions on such Exercise Date by the lower of (i) 85 percent of the Fair Market Value of the Common Stock on the Offering Date, or (ii) 85 percent of the Fair Market Value of the Common
Stock on the Exercise Date, (b) a number of shares of Common Stock determined by dividing $25,000 by the Fair Market Value of the Common Stock on the Offering Date of such Offering; or (c) such other lesser maximum number of shares as
shall have been established by the Administrator in advance of the Offering; provided, however, that such Option shall be subject to the limitations set forth below. Each Participant’s Option shall be exercisable only to the extent of such
Participant’s accumulated payroll deductions on the Exercise Date. The purchase price for each share purchased under each Option (the “Option Price”) will be 85 percent of the Fair Market Value of the Common Stock on the
Offering Date or the Exercise Date, whichever is less. 
 Notwithstanding the foregoing, no Participant may be granted an option hereunder
if such Participant, immediately after the option was granted, would be treated as owning stock possessing 5 percent or more of the total combined voting power or value of all classes of stock of the Company or any Parent or Subsidiary (as
defined in Section 11). For purposes of the preceding sentence, the attribution rules of Section 424(d) of the Code shall apply in determining the stock ownership of a Participant, and all stock which the Participant has a contractual
right to purchase shall be treated as stock owned by the Participant. In addition, no Participant may be granted an Option which permits his or her rights to purchase stock under the Plan, and any other employee stock purchase plan of the Company
and its Parents and Subsidiaries, to accrue at a rate which exceeds $25,000 of the fair market value of such stock (determined on the option 

  
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grant date or dates) for each calendar year in which the Option is outstanding at any time. The purpose of the limitation in the preceding sentence is to comply with Section 423(b)(8) of the
Code and shall be applied taking Options into account in the order in which they were granted. 
 9.    Exercise of
Option and Purchase of Shares. Each employee who continues to be a Participant in the Plan on the Exercise Date shall be deemed to have exercised his or her Option on such date and shall acquire from the Company such number of whole shares of
Common Stock reserved for the purpose of the Plan as his or her accumulated payroll deductions on such date will purchase at the Option Price, subject to any other limitations contained in the Plan. Any amount remaining in a Participant’s
account at the end of an Offering solely by reason of the inability to purchase a fractional share will be carried forward to the next Offering; any other balance remaining in a Participant’s account at the end of an Offering will be refunded
to the Participant promptly. 
 10.    Issuance of Certificates. Certificates representing shares of Common Stock
purchased under the Plan may be issued only in the name of the employee, in the name of the employee and another person of legal age as joint tenants with rights of survivorship, or in the name of a broker authorized by the employee to be his, her
or their, nominee for such purpose. 
 11.    Definitions. 

“Compensation” means the amount of base pay, prior to salary reduction pursuant to Sections 125, 132(f) or 401(k) of the Code,
but excluding overtime, commissions, incentive or bonus awards, allowances and reimbursements for expenses such as relocation allowances or travel expenses, income or gains on the exercise of Company stock options, and similar items. 

“Designated Subsidiary” means any present or future Subsidiary (as defined below) that has been designated by the Board to
participate in the Plan. The Board may so designate any Subsidiary, or revoke any such designation, at any time and from time to time, either before or after the Plan is approved by the stockholders. 

  
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 “Fair Market Value of the Common Stock” on any given date means the fair market
value of the Common Stock determined in good faith by the Administrator; provided, however, that if the Common Stock is admitted to quotation on the National Association of Securities Dealers Automated Quotation System (“NASDAQ”),or
another national securities exchange, the determination shall be made by reference to the closing price on such date. If there is no closing price for such date, the determination shall be made by reference to the last date preceding such date for
which there is a closing price. 
 “Initial Public Offering” means the first underwritten, firm commitment public offering
pursuant to an effective registration statement under the Securities Act of 1933, as amended, covering the offer and sale by the Company of its Common Stock. 

“Parent” means a “parent corporation” with respect to the Company, as defined in Section 424(e) of the Code. 

“Participant” means an individual who is eligible as determined in Section 3 and who has complied with the provisions of
Section 4. 
 “Registration Date” means the date the registration statement on Form
S-1 that is filed by the Company with respect to the Initial Public Offering is declared effective by the Securities and Exchange Commission. 

“Subsidiary” means a “subsidiary corporation” with respect to the Company, as defined in Section 424(f) of the Code.

 12.    Rights on Termination of Employment. If a Participant’s employment terminates for any reason
before the Exercise Date for any Offering, no payroll deduction will be taken 

  
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from any pay due and owing to the Participant and the balance in the Participant’s account will be paid to such Participant or, in the case of such Participant’s death, to his or her
designated beneficiary as if such Participant had withdrawn from the Plan under Section 7. An employee will be deemed to have terminated employment, for this purpose, if the corporation that employs him or her, having been a Designated
Subsidiary, ceases to be a Subsidiary, or if the employee is transferred to any corporation other than the Company or a Designated Subsidiary. An employee will not be deemed to have terminated employment for this purpose, if the employee is on an
approved leave of absence for military service or sickness or for any other purpose approved by the Company, if the employee’s right to reemployment is guaranteed either by a statute or by contract or under the policy pursuant to which the
leave of absence was granted or if the Administrator otherwise provides in writing. 
 13.    Special Rules.
Notwithstanding anything herein to the contrary, the Administrator may adopt special rules applicable to the employees of a particular Designated Subsidiary, whenever the Administrator determines that such rules are necessary or appropriate for the
implementation of the Plan in a jurisdiction where such Designated Subsidiary has employees; provided that such rules are consistent with the requirements of Section 423(b) of the Code. Any special rules established pursuant to this
Section 13 shall, to the extent possible, result in the employees subject to such rules having substantially the same rights as other Participants in the Plan. 

14.    Optionees Not Stockholders. Neither the granting of an Option to a Participant nor the deductions from his
or her pay shall constitute such Participant a holder of the shares of Common Stock covered by an Option under the Plan until such shares have been purchased by and issued to him or her. 

  
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 15.    Rights Not Transferable. Rights under the Plan are not
transferable by a Participant other than by will or the laws of descent and distribution, and are exercisable during the Participant’s lifetime only by the Participant. 

16.    Application of Funds. All funds received or held by the Company under the Plan may be combined with other
corporate funds and may be used for any corporate purpose. 
 17.    Adjustment in Case of Changes Affecting Common
Stock. In the event of a subdivision of outstanding shares of Common Stock, the payment of a dividend in Common Stock or any other change affecting the Common Stock, the number of shares approved for the Plan and the share limitation set forth
in Section 8 shall be equitably or proportionately adjusted to give proper effect to such event. 

18.    Amendment of the Plan. The Board may at any time and from time to time amend the Plan in any respect, except
that without the approval within 12 months of such Board action by the stockholders, no amendment shall be made increasing the number of shares approved for the Plan or making any other change that would require stockholder approval in order for the
Plan, as amended, to qualify as an “employee stock purchase plan” under Section 423(b) of the Code. 

19.    Insufficient Shares. If the total number of shares of Common Stock that would otherwise be purchased on any
Exercise Date plus the number of shares purchased under previous Offerings under the Plan exceeds the maximum number of shares issuable under the Plan, the shares then available shall be apportioned among Participants in proportion to the amount of
payroll deductions accumulated on behalf of each Participant that would otherwise be used to purchase Common Stock on such Exercise Date. 

  
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 20.    Termination of the Plan. The Plan may be terminated at any
time by the Board. Upon termination of the Plan, all amounts in the accounts of Participants shall be promptly refunded. 

21.    Governmental Regulations. The Company’s obligation to sell and deliver Common Stock under the Plan is
subject to obtaining all governmental approvals required in connection with the authorization, issuance, or sale of such stock. 

22.    Governing Law. This Plan and all Options and actions taken thereunder shall be governed by, and construed in
accordance with, the laws of the State of Delaware, applied without regard to conflict of law principles. 

23.    Issuance of Shares. Shares may be issued upon exercise of an Option from authorized but unissued Common
Stock, from shares held in the treasury of the Company, or from any other proper source. 
 24.    Tax
Withholding. Participation in the Plan is subject to any minimum required tax withholding on income of the Participant in connection with the Plan. Each Participant agrees, by entering the Plan, that the Company and its Subsidiaries shall have
the right to deduct any such taxes from any payment of any kind otherwise due to the Participant, including shares issuable under the Plan. 

25.    Notification Upon Sale of Shares. Each Participant agrees, by entering the Plan, to give the Company prompt
notice of any disposition of shares purchased under the Plan where such disposition occurs within two years after the date of grant of the Option pursuant to which such shares were purchased or within one year after the date such shares were
purchased. 
 26.    Effective Date and Approval of Shareholders. The Plan shall take effect on the date
immediately preceding the Registration Date, subject to approval by the holders of a majority of the votes cast at a meeting of stockholders at which a quorum is present or by written consent of the stockholders. 

  
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 DATE APPROVED BY BOARD OF DIRECTORS: September 17, 2020, and effective upon consummation of the
Company’s initial public offering. 
 DATE APPROVED BY STOCKHOLDERS: October 2, 2020, and effective upon consummation of the Company’s
initial public offering. 

  
 11EX-10.4

 Exhibit 10.4 

CODIAK BIOSCIENCES, INC. 

NON-EMPLOYEE DIRECTOR COMPENSATION PRACTICES 

The purpose of this Non-Employee Director Compensation Practices (the “Practices”) of Codiak
BioSciences, Inc., a Delaware corporation (the “Company”), is to provide a total compensation package that enables the Company to attract and retain, on a long-term basis, high-caliber directors who are not employees or officers of
the Company. This Practices will become effective as of the effective time of the registration statement for the Company’s initial firm commitment underwritten public offering of equity securities (the “Effective Date”) and
will apply to all non-employee directors of the Company (such directors, the “Eligible Directors”) of the Company (the “Board”). In furtherance of this purpose, except as
otherwise provided in any written agreement between the Company and an Eligible Director, all Eligible Directors shall be paid compensation for services provided to the Company as set forth below: 

Cash Retainers 
 Annual Retainer for Board
Membership: $35,000 for general availability and participation in meetings and conference calls of our Board. No additional compensation for attending individual Board meetings. 

 

					
	 Additional Annual Retainer for Non-Executive Chair of
the Board:
	  	$	30,000	 
		
	 Additional Annual Retainers for Committee Membership:
	  			
		
	 Audit Committee Chairperson:
	  	$	15,000	 
		
	 Audit Committee member:
	  	$	7,500	 
		
	 Compensation Committee Chairperson:
	  	$	10,000	 
		
	 Compensation Committee member:
	  	$	5,000	 
		
	 Nominating and Corporate Governance Committee Chairperson:
	  	$	8,000	 
		
	 Nominating and Corporate Governance Committee member:
	  	$	4,000	 

 No additional compensation for attending individual committee meetings. All cash retainers will be paid
quarterly, in arrears, or upon the earlier of resignation or removal of the Eligible Director. Cash retainers owing to Eligible Directors shall be annualized, meaning that with respect to Eligible Directors who join the Board during the calendar
year, and with respect to all Eligible Directors for 2020, such amounts shall be pro-rated based on the number of calendar days served by such Eligible Director following the Effective Date. 

Equity Retainers 
 Initial Equity Grant: For
each Eligible Director joining the Board after the Effective Date, upon his or her initial appointment to the Board, each such Eligible Director shall receive a one-time equity grant of an option to purchase
20,000 shares of the Company’s common stock, par value 

 
$0.0001 per share (the “Common Stock”). Such initial equity grant shall vest in equal quarterly installments during the twelve quarters following the grant date, subject to the
Eligible Director’s continued service on the Board through each such date. 
 Annual Equity Grant: Immediately following each annual meeting of
the Company’s stockholders, each continuing Eligible Director who has served as a director for the previous six months will receive an annual equity grant of an option to purchase 10,000 shares of Common Stock. Such annual equity grant shall
vest on the earlier of the one-year anniversary of the grant date or the Company’s next annual meeting of stockholders, subject to the Eligible Director’s continued service on the Board through such
date. All of the foregoing option grants will become immediately exercisable upon the Eligible Director’s death or upon a Sale Event (as defined in the Company’s 2020 Stock Option and Incentive Plan). 

Any stock option granted to an Eligible Director pursuant to this Practices will be granted at an exercise price equal to the fair market value of a share of
Common Stock on the date of grant. 
 Expenses 

The Company shall reimburse all reasonable out-of-pocket expenses incurred by
Eligible Directors in attending Board and committee meetings. 
 ADOPTED: September 17, 2020

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