Exhibit 10.1

SEPARATION, TRANSITION, AND RELEASE OF CLAIMS AGREEMENT

This Separation, Transition and Release of Claims Agreement (the “Agreement”) is
made by and between Oliver S. Fetzer, Ph.D (the “Employee”) and Cerulean Pharma
Inc. (“Cerulean” or the “Company”) (together, the “Parties”).

WHEREAS, the Employee has been employed as the President and Chief Executive
Officer of the Company since 2009;

WHEREAS, the Parties entered into an Amended and Restated Executive Employment
Agreement effective as of June 24, 2014 (the “Employment Agreement”);

WHEREAS, the Employee is resigning from his employment with the Company and as
an officer and director of the Company and any affiliate, in each case effective
October 29, 2014 (the “Separation Date”); and

WHEREAS, in the interest of an amicable departure and transition, and in
exchange for, among other things, the Employee entering into and complying with
this Agreement and providing the post-employment assistance set forth below, the
Company is providing the Employee with consideration set forth in this
Agreement.

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency
of which is hereby acknowledged, the Parties hereby agree as follows:

1. Resignation from Employment and Director and Officer Positions. As of the
Separation Date, the Employee hereby resigns from his employment with the
Company and from his positions as a member of the Company’s Board of Directors
and as an officer of the Company, as well as from any other director or officer
positions he holds with any of the Company’s subsidiaries or entities affiliated
with the Company. The Employee agrees to execute and deliver any documents
reasonably necessary to effectuate such resignations, provided that nothing in
any such document is inconsistent with any terms set forth in this Agreement.
Should the Employee fail to promptly submit on the Separation Date his
resignation as an officer or director or execute any documents requested by the
Company or any Company affiliate to effectuate the Employee’s resignation from
any and all officer and director positions, the Employee hereby irrevocably
appoints the Company to be his attorney-in-fact to execute any documents and do
anything in his name to effect such resignation. A written notification signed
by a director or duly authorized officer of the Company that any instrument,
document or act falls within the authority conferred by this subsection will be
conclusive evidence that it does so. The Company will prepare any documents, pay
any filing fees, and bear any other expenses related to this section.

2. Post-Employment Consulting and Assistance. In order to assist the Company in
making a smooth transition to new leadership, the Employee agrees that, for one
hundred and eighty (180) days following the Separation Date (the “Consulting
Period”), he shall make himself reasonably available by telephone or e-mail from
time to time, upon reasonable notice and on an as-needed basis, to consult with
the Company and to provide any reasonable information and/or guidance that the
Company may request concerning his former duties and responsibilities and/or his
knowledge of the Company’s business and operations (the

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“Post-Employment Assistance”). The Employee acknowledges and agrees that the
consideration set forth in this Agreement is being provided, in part, as
consideration for this Post-Employment Assistance, and that he will not be
entitled to receive any additional compensation or benefits for such assistance.

3. Stock Options. The Employee and Company hereby agree that, notwithstanding
any term of any outstanding stock option held by the Employee or in any other
agreement between the Company and the Employee, any and all such stock options
shall cease vesting as of the Separation Date and will remain exercisable during
the Consulting Period, but not for any period following the Consulting Period
(and in no event later than the Final Exercise Date (as defined in the
Employee’s applicable option agreement(s))).

4. Releases of Claims.

(a) By the Employee - In exchange for the consideration set forth in this
Agreement, which the Employee acknowledges he would not otherwise be entitled to
receive, the Employee hereby fully, forever, irrevocably and unconditionally
releases, remises and discharges the Company, its affiliates, subsidiaries,
parent companies, predecessors, and successors, and all of its and their
respective past and present officers, directors, stockholders, partners,
members, employees, agents, representatives, plan administrators, attorneys,
insurers and fiduciaries (each in their individual and corporate capacities)
(collectively, the “Released Parties”) from any and all claims, complaints,
demands, actions, causes of action, suits, rights, debts, sums of money, costs,
accounts, reckonings, covenants, contracts, agreements, promises, doings,
omissions, damages, executions, obligations, liabilities, and expenses
(including attorneys’ fees and costs), of every kind and nature, whether known
or unknown, that the Employee ever had or now has against any or all of the
Released Parties, including, but not limited to, any and all claims arising out
of or relating to the Employee’s employment with and/or service as an officer
and/or director of the Company or any affiliate, or to the Employee’s separation
from employment with and/or service as an officer and/or director of the Company
or any affiliate, including, but not limited to, all claims under Title VII of
the Civil Rights Act of 1964, 42 U.S.C. § 2000e et seq., the Americans With
Disabilities Act of 1990, 42 U.S.C. § 12101 et seq., the Genetic Information
Nondiscrimination Act of 2008, 42 U.S.C. § 2000ff et seq., the Family and
Medical Leave Act, 29 U.S.C. § 2601 et seq., the Worker Adjustment and
Retraining Notification Act (“WARN”), 29 U.S.C. § 2101 et seq., the
Rehabilitation Act of 1973, 29 U.S.C. § 701 et seq., Executive Order 11246,
Executive Order 11141, the Fair Credit Reporting Act, 15 U.S.C. § 1681 et seq.,
and the Employee Retirement Income Security Act of 1974 (“ERISA”), 29 U.S.C. §
1001 et seq., all as amended; all claims arising out of the Massachusetts Fair
Employment Practices Act., Mass. Gen. Laws ch. 151B, § 1 et seq., the
Massachusetts Civil Rights Act, Mass. Gen. Laws ch. 12, §§ 11H and 11I, the
Massachusetts Equal Rights Act, Mass. Gen. Laws. ch. 93, § 102 and Mass. Gen.
Laws ch. 214, § 1C, the Massachusetts Labor and Industries Act, Mass. Gen. Laws
ch. 149, § 1 et seq., the Massachusetts Wage Act, Mass. Gen. Laws ch. 149, § 148
et seq. (Massachusetts law regarding payment of wages and overtime), Mass. Gen.
Laws ch. 214, § 1B (Massachusetts right of privacy law), the Massachusetts
Maternity Leave Act, Mass. Gen. Laws ch. 149, § 105D, and the Massachusetts
Small Necessities Leave Act, Mass. Gen. Laws ch. 149, § 52D, all as

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amended; all common law claims including, but not limited to, actions in
defamation, intentional infliction of emotional distress, misrepresentation,
fraud, wrongful discharge, and breach of contract (including, without
limitation, any claims arising out of or relating to the Employment Agreement);
all state and federal whistleblower claims to the maximum extent permitted by
law; all claims to any non-vested ownership interest in the Company, contractual
or otherwise; and any claim or damage arising out of the Employee’s employment
with and/or separation from the Company or any affiliate (including a claim for
retaliation) under any common law theory or any federal, state or local statute
or ordinance not expressly referenced above; provided, however, that nothing in
this Agreement prevents the Employee from filing a charge with, cooperating
with, or participating in any proceeding before the Equal Employment Opportunity
Commission or a state fair employment practices agency (except that the Employee
acknowledges that he may not recover any monetary benefits in connection with
any such claim, charge or proceeding and further waives any rights or claims to
any payment, benefit, attorneys’ fees or other remedial relief in connection
with any such claim, charge or proceeding), or releases, remises or discharges
any rights of the Employee to (i) vested ownership interests in the Company,
(ii) vested benefit entitlements, or (iii) indemnification or liability
insurance coverage, as provided for by the Indemnification Agreement between the
Employee and the Company, the by-laws or policies of the Company or its
affiliates, or applicable law.

(b) By the Company - The Company hereby fully, forever, irrevocably and
unconditionally releases, remises and discharges the Employee from any and all
claims, complaints, demands, actions, causes of action, suits, rights, debts,
sums of money, costs, accounts, reckonings, covenants, contracts, agreements,
promises, doings, omissions, damages, executions, obligations, liabilities, and
expenses (including attorneys’ fees and costs), of every kind and nature,
whether known or unknown, that the Company ever had or now has against the
Employee, including, but not limited to, any and all claims arising out of or
relating to the Employee’s employment with and/or service as an officer and/or
director of the Company or any affiliate, or Employee’s separation from
employment with and/or service as an officer and/or director of the Company or
any affiliate; provided, however, that notwithstanding the foregoing, the
Company does not release the Employee from his continuing obligations as set
forth in paragraph 5 below, from any claims for fraud or embezzlement, from any
civil claims based on any acts and/or omissions that satisfy the elements of a
criminal offense, or from any claims arising out of any deliberate misconduct by
the Employee that resulted in injury to the Company (provided that the Company
hereby represents that it knows of no such claims), nor does the Company release
the Employee with respect to any clawback of the Employee’s compensation to the
extent required by the Sarbanes-Oxley Act, the Dodd-Frank Wall Street Reform and
Consumer Protection Act, or any other applicable law.

5. Continuing Obligations. The Employee acknowledges his obligation to keep
confidential and not to use or disclose any and all non-public information
concerning the Company that he acquired during the course of his employment with
and/or service as an officer or director of the Company, including, but not
limited to, any non-public information concerning the Company’s business
affairs, business prospects, and financial condition. The Employee further
acknowledges and reaffirms his obligations under the Invention and
Non-Disclosure Agreement he previously executed for the benefit of the Company,
which remain in full force and effect.

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6. Return of Company Property. The Employee hereby confirms that he has returned
to the Company all keys, files, records (and copies thereof), equipment
(including, but not limited to, computer hardware, software and printers,
wireless handheld devices, USB storage devices, cellular phones, tablets, etc.),
Company identification, Company vehicles and any other Company-owned property in
his possession or control and that he has left intact all electronic Company
documents, including but not limited to, those that he developed or helped to
develop during his employment and/or his role as an officer or director of the
Company. The Employee further confirms that he has canceled all accounts for his
benefit, if any, in the Company’s name, including but not limited to, credit
cards, telephone charge cards, cellular phone, wireless data or internet
accounts, and/or and computer accounts.

7. Nondisparagement. The Employee understands and agrees that, to the extent
permitted by law, he shall not make any false, disparaging, derogatory or
defamatory statements to any person or entity, including, without limitation,
any media outlet, industry group, financial institution or current or former
employee, consultant, client or customer of the Company or any affiliate,
regarding the Company or any affiliate or any of its or their respective
directors, officers, employees, agents or representatives or about the Company’s
or any affiliate’s business affairs or financial condition; provided, however,
that nothing herein shall be construed as preventing the Employee from making
truthful disclosures to any governmental entity or in any litigation or
arbitration. The Company agrees that it will instruct its current officers and
directors to refrain from making any false, disparaging or derogatory statements
to any person or entity, including, without limitation, any media outlet,
industry group, financial institution or current or former employee, consultant,
client or customer of the Company or any Company affiliate about the Employee;
provided, however, that nothing herein shall be construed as requiring the
Company to instruct any person not to make truthful disclosures to any
governmental entity or in any litigation or arbitration.

8. Cooperation. To the extent permitted by law, the Employee agrees to
reasonably cooperate with the Company in the investigation, defense or
prosecution of any claims or actions now in existence or that may be brought in
the future against or on behalf of the Company or any affiliate that involve
matters relating to the Employee’s role as a director, officer, or employee of
the Company or any affiliate. The Employee’s cooperation in connection with such
claims or actions shall include, but not be limited to, being reasonably
available to meet with the Company’s counsel to prepare for discovery or any
mediation, arbitration, trial, administrative hearing or other proceeding or to
act as a witness when reasonably requested by the Company. The Employee further
agrees that, to the extent permitted by law, he will notify the Company promptly
in the event that he is served with a subpoena or in the event that he is asked
to provide a third party with information concerning any actual or potential
complaint or claim against the Company or any affiliate. The Employee shall be
entitled to receive reimbursement of all reasonable out of pocket expenses
incurred by the Employee in cooperating hereunder, including expenses related to
travel and other expenses while away from home, plus a reasonable hourly fee,
provided, however, that the Company will not pay the Employee a fee for time
spent providing testimony in any arbitration, trial, administrative hearing or
other proceeding. The Company shall reimburse such expenses subject to its
expense reimbursement policy.

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9. Time for Consideration; Effective Date. To accept this Agreement, the
Employee must sign and return this Agreement so that it is received by the
Company’s General Counsel on, but not before, October 29, 2014.

10. Business Expenses and Final Compensation. The Employee acknowledges that he
has been reimbursed by the Company for all business expenses incurred in
conjunction with the performance of his employment and that no other
reimbursements are owed to him. The Employee further acknowledges that he has
received payment in full for all services rendered in conjunction with his
employment by and/or service as an officer or director of the Company and/or any
affiliate, including, without limitation, payment for all wages, bonuses,
equity, commissions and accrued, unused vacation time, and that no other
compensation or consideration is owed to him except as explicitly set forth
herein.

11. Nature of Agreement. The Parties understand and agree that this Agreement is
a separation agreement and does not constitute an admission of liability or
wrongdoing on the part of either Party.

12. Amendment. This Agreement shall be binding upon the Parties and may not be
modified in any manner, except by an instrument in writing of concurrent or
subsequent date signed by duly authorized representatives of the Parties hereto.
This Agreement is binding upon and shall inure to the benefit of the Parties and
their respective agents, assigns, heirs, executors, successors and
administrators.

13. Waiver of Rights. No delay or omission by either Party in exercising any
right under this Agreement shall operate as a waiver of that or any other right.
A waiver or consent given by a Party on any one occasion shall be effective only
in that instance and shall not be construed as a bar to or waiver of any right
on any other occasion.

14. Validity. Should any provision of this Agreement be declared or be
determined by any court of competent jurisdiction to be illegal or invalid, the
validity of the remaining parts, terms or provisions shall not be affected
thereby and said illegal or invalid part, term or provision shall be deemed not
to be a part of this Agreement.

15. Acknowledgements. The Employee acknowledges that he has been given a
reasonable period of time to consider this Agreement and that the Company is
hereby advising him to consult with an attorney of his own choosing prior to
signing this Agreement.

16. Voluntary Assent. The Employee affirms that no other promises or agreements
of any kind have been made to or with him by any person or entity whatsoever to
cause him to sign this Agreement, and that he fully understands the meaning and
intent of this Agreement. The Employee states and represents that he has had an
opportunity to fully discuss and review the terms of this Agreement with an
attorney. The Employee further states and represents that he has carefully read
this Agreement, understands the contents herein, freely and voluntarily assents
to all of the terms and conditions hereof, and signs his name of his own free
act.

17. Applicable Law. This Agreement shall be governed by the laws of the
Commonwealth of Massachusetts without regard to conflict of laws provisions. The
Parties hereby irrevocably submit to and acknowledge and recognize the
jurisdiction of the courts of the

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Commonwealth of Massachusetts, or if appropriate, a federal court located in the
Commonwealth of Massachusetts (which courts, for purposes of this Agreement, are
the only courts of competent jurisdiction), over any suit, action or other
proceeding arising out of, under or in connection with this Agreement or the
subject matter hereof.

18. Tax Acknowledgement. The Employee acknowledges that he is not relying upon
the advice or representation of the Company with respect to the tax treatment of
any of the consideration set forth herein.

19. Entire Agreement. This Agreement contains and constitutes the entire
understanding and agreement between the Parties hereto with respect to the
Employee’s separation and the settlement of claims against the Company and
cancels all previous oral and written negotiations, agreements, commitments and
writings in connection therewith.

20. Counterparts. This Agreement may be executed in any number of counterparts,
each of which when so executed and delivered shall be taken to be an original,
but all of which together shall constitute one and the same document. Facsimile
and PDF signatures shall be deemed to be of equal force and effect as originals.

IN WITNESS WHEREOF, the Parties, intending to be legally bound, have executed
this Agreement on the date(s) indicated below.

 

CERULEAN PHARMA INC.

/s/ Robert Tepper

   

October 29, 2014

Robert Tepper     Date Chair of the Compensation Committee     I HEREBY AGREE TO
THE TERMS AND CONDITIONS SET FORTH ABOVE.

/s/ Oliver S. Fetzer

   

October 29, 2014

Oliver S. Fetzer, Ph.D     Date