<PAGE>

                                                                    EXHIBIT 10.2

                              EMPLOYMENT AGREEMENT

          This Employment Agreement (the "Agreement"), is made and entered into
this 15th day of December 2005, by and between Archemix Corp. (which, together
with any parent companies, subsidiaries, affiliates, successors and assigns
shall be referred to as "Archemix" or the "Company"), with its principal offices
located at One Hampshire Street, Cambridge, MA 02139 and John Duncan Higgons
(the "Employee").

                                   WITNESSETH

          WHEREAS, the Company has a need for the Employee's professional and
personal services in an executive capacity; and

          WHEREAS, the Employee and the Company desire to enter into a formal
Employment Agreement to fully recognize the anticipated contributions of the
Employee to the Company and to assure continuous, harmonious conduct of the
Company's business.

          NOW, THEREFORE, in consideration of the mutual promises, terms,
provisions, and conditions contained herein and for other good and valuable
consideration, the receipt and sufficiency of which are hereby mutually
acknowledged, the parties agree as follows:

     1.   POSITION. Subject to the terms and conditions of this Agreement, the
          Company will employ the Employee, and the Employee will be employed by
          the Company as Executive Vice President, Business Operations ("EVP").
          The Employee's responsibilities shall include any responsibilities
          normally associated with such position and any other responsibilities
          assigned reasonably by the Board of Directors (the "Board"). The
          Employee's position and assignments are subject to change.

     2.   DEVOTION TO DUTIES. Except for vacations and absences due to temporary
          illness in accordance with the policies of the Company, while the
          Employee is employed hereunder, the Employee will use best efforts to
          perform faithfully all duties assigned to the Employee pursuant to
          this Agreement and to devote the Employee's full business time and
          energies to the business and affairs of the Company; provided,
          however, that the Employee may, with the prior written consent of the
          Board, engage in other business activities which do not conflict with
          the Employee's duties hereunder, whether or not such activity is
          pursued for gain, profit or other pecuniary advantage. While the
          Employee is employed hereunder, the Employee will not serve as an
          employee, consultant, director or advisor to any person or entity
          without the prior written consent of the Company.

     3.   TERM AND TERMINATION. The Employee's employment with Archemix shall
          commence on February 1, 2006 (the "Employee's Starting Date") and
          shall be considered at-will employment, which may be terminated by the
          Employee or Archemix at any time for any reason. In the event that the
          Employee is terminated, the Employee shall be entitled to severance
          pay equal to nine (9) months Base Salary and a pro-rata Annual Bonus
          with the respect to the year in which the termination of employment
          occurred (calculated by multiplying the target Annual Bonus by a
          fraction, the numerator of which shall be the

<PAGE>

          number of days worked in the current calendar year of the termination
          of employment and the denominator of which shall be 365) plus
          continued vesting of the Option for this 9-month period (collectively
          the "Severance Package"). The foregoing notwithstanding the Employee
          shall not be entitled to receive the Severance Package if the Employee
          is terminated for Cause. For purposed of this Agreement "Cause" shall
          mean any of the following (each of which shall be determined in the
          sole discretion of the Company): (a) a continuing failure by the
          Employee to render services to the Company in accordance with the
          Employee's assigned duties (other than such a failure as a result of
          the Employee's death or disability); (b) any act or omission by the
          Employee involving misconduct or negligence which results in material
          harm to the Company; (c) the Employee's commission of any felony or
          any fraud, financial wrongdoing, disloyalty, dishonesty or breach of
          fiduciary duty in connection with the performance of the Employee's
          obligations to the Company and which adversely affects the business
          activities, reputation or goodwill of the Company; (d) the Employee's
          deliberate disregard of a Company rule or policy which materially and
          adversely affects the business activities, reputation, or goodwill of
          the Company; or (e) the Employee's material breach of this Agreement.
          In the event of a termination for Cause, the Employee shall receive a
          written termination notice from the Company stating that the
          termination of employment is "for Cause." Such written notice shall
          specify the particular act or acts, or failure to act, which is or are
          the basis for the decision to so terminate the Employee's employment
          for Cause. The Employee shall be given the opportunity within fifteen
          (15) calendar days of the receipt of such notice to meet with the
          Board or its appropriate designee to defend such act or acts, or
          failure to act, and the Employee shall be given fifteen (15) calendar
          days after such meeting (the "Cure Period") to cure such act (or
          failure to act) to the Board's or its appropriate designee's
          reasonable satisfaction. Upon failure of the Employee, within such
          Cure Period, to so cure such act or failure to act, the Employee's
          employment by the Company shall be deemed terminated for Cause.

     4.   COMPENSATION AND BENEFITS.

               a.   Base Salary. The Employee's initial base pay shall be at a
                    gross rate of 23,750 per month (the "Base Salary"), minus
                    customary deductions for federal and state taxes plus any
                    elective benefits or deductions.

               b.   Bonus. In addition to the Base Salary, the Employee shall be
                    eligible to receive an annual bonus for each calendar year
                    that the Employee completes with the Company (the "Annual
                    Bonus"). The award, amount and composition (e.g. cash and/or
                    option to purchase common stock) of any Annual Bonus shall
                    be determined by and in the sole discretion of the Board or
                    its designee(s), with a target amount equal to twenty seven
                    percent (27%) of the Base Salary earned during the year to
                    which the Annual Bonus relates.

               c.   Options. Subject to approval by the Board of Directors (or
                    an appropriate Committee appointed by the Board of
                    Directors), and pursuant to a written stock option agreement
                    entered into by and between the Employee and the Company
                    (the "Option Agreement") pursuant to the Corporation's 2001
                    Employee, Director and Consultant Stock Plan, as amended
                    (the "2001 Plan"), Archemix will grant


                                        2

<PAGE>

                    the Employee an option to purchase one million two hundred
                    thousand (1,200,000) shares of Archemix Common Stock (the
                    "Option"). The exercise price of the Option will be the fair
                    market value of the Company's Common Stock on the date the
                    Option is granted and such Option shall be subject to the
                    terms and conditions of the Option as set forth in the 2001
                    Plan and the Option Agreement. To the extent permissible
                    under applicable federal tax law, the Option will be an
                    incentive stock option with the Option vesting on the
                    following schedule: twenty-five percent (25%) of such shares
                    shall vest on the first (1st) anniversary of the date of the
                    Employee's option agreement; after the first (1st)
                    anniversary, the remaining seventy-five percent (75%) of
                    such shares shall vest ratably in three (3) month periods
                    until the fourth (4th) anniversary the Employee's option
                    agreement. Such vesting shall commence on the first
                    anniversary of February 1, 2006 and quarterly thereafter. In
                    the event of a Change of Control (as defined below) occurs
                    within twelve (12) months of Employee's Starting Date, a
                    portion of the Employee's Option shall accelerate in
                    accordance with the aforementioned schedule so as to vest
                    for a time period equal to the Employee's actual period of
                    employment plus an additional twelve (12) months (the
                    "Vesting Time"). For purposes of clarification, upon a
                    Change of Control the Employee shall be entitled to exercise
                    an option to purchase the number of shares he would have
                    otherwise been entitled to purchase had he remained employed
                    by the Company for the Vesting Time. If no Change of Control
                    occurs within twelve (12) months of Employee's Starting
                    Date, the Employee shall not be entitled to any acceleration
                    and vesting of the Option under the terms of this Agreement.
                    For purposes of this Agreement, "Change of Control" shall
                    mean the closing of a sale, merger, joint venture, tender
                    offer or otherwise, in which 50% or more of the outstanding
                    equity securities of the Company or 50% or more of the
                    voting power of the Company is acquired by a third party, or
                    all or substantially all of the Company's business or assets
                    are sold to, combined with, or transferred to a third party.

               d.   Vacation. The Employee will be entitled to three (3) weeks
                    paid vacation in each calendar year and paid holidays and
                    personal days in accordance with the Company's policies as
                    in effect from time to time. In addition, the Employee shall
                    be entitled to unpaid leave for the following dates:
                    February 20, 2006 through February 24, 2006; May 22, 2006
                    through June 9, 2006; and 15 working days to be taken in
                    August 2006 at the Employee's discretion and election.

               e.   Fringe Benefits. The Employee will be entitled to
                    participate in any employee benefit plans which the Company
                    provides or may establish for the benefit of its employees
                    generally (including, but not limited to, group life,
                    disability, medical, dental and other insurance, retirement,
                    pension, profit-sharing and similar plans) (collectively,
                    the "Fringe Benefits"), provided that the Fringe Benefits
                    will not include any stock option or similar plans relating
                    to the grant of equity securities of the Company except as
                    provided herein. The Employee's eligibility to participate
                    in the Fringe Benefits and receive benefits thereunder will
                    be subject to the plan documents governing such Fringe
                    Benefits. Nothing contained herein will require the Company
                    to establish or maintain Fringe Benefits.


                                        3

<PAGE>

     5.   CONFIDENTIALITY, NON-COMPETITION AND INVENTIONS. The Company considers
          the protection of its confidential information, proprietary materials
          and goodwill to be extremely important. As such the Employee may not
          discuss the fact or terms of this Agreement with anyone other than the
          executive officers of the Company and members of the Employee's
          immediate family (and, if relevant, the Employee's recruiting firm,
          financial advisor or lawyer). In addition the Employee will be
          required to sign an agreement relating to confidentiality,
          non-competition, non-solicitation and work product prior to
          commencement of employment. Such agreement shall be considered
          integrated with and part of this Agreement.

     6.   RECORDS. Upon termination of the Employee's employment hereunder or at
          any other time as requested by the Company, the Employee will deliver
          to the Company any property in the Employee's possession or control,
          including but not limited to products, materials, memoranda,
          electronic files, notes, records, reports or other documents or
          photocopies of the same.

     7.   REPRESENTATIONS. The Employee hereby represents and warrants to the
          Company that the Employee understands this Agreement, that the
          Employee has entered into this Agreement voluntarily and that the
          Employee has no commitments or obligations inconsistent with this
          Agreement. The Employee agrees to indemnify and hold the Company
          harmless against loss, damage, liability or expense arising from any
          claim based upon circumstances alleged to be inconsistent with such
          representations and warranties.

     8.   GENERAL.

               a.   Notices. All notices, requests, consents and other
                    communications hereunder will be deemed to have been given
                    either (i) if by hand, at the time of the delivery thereof
                    to the receiving party at the address of such party set
                    forth above, (ii) if sent by overnight courier, on the next
                    business day following the day such notice is delivered to
                    the courier service, or (iii) if sent by registered or
                    certified mail, on the fifth business day following the day
                    such mailing is made. Any notice from the Employee to the
                    Company must be explicitly directed to the attention of the
                    Board or such other designee.

               b.   Entire Agreement. This Agreement, together with the other
                    agreements specifically referred to herein, embodies the
                    entire agreement and understanding between the parties and
                    supersedes all prior oral or written agreements and
                    understandings. No statement, representation, warranty,
                    covenant or agreement of any kind not expressly set forth in
                    this Agreement will affect, or be used to interpret, change
                    or restrict the express terms and provisions of this
                    Agreement.

               c.   Assignment. The Company may assign its rights and
                    obligations hereunder to any person or entity that succeeds
                    to all or substantially all of the Company's business or
                    that aspect of the Company's business in which the Employee
                    is substantially involved. The Employee may not assign any
                    rights and obligations under this Agreement without the
                    prior written consent of the Company.


                                        4

<PAGE>

               d.   Benefit. All statements, representations, warranties,
                    covenants and agreements in this Agreement will be binding
                    on the parties and will inure to the benefit of the
                    respective successors and permitted assigns of each party.
                    Nothing in this Agreement will be construed to create any
                    rights or obligations except between the Company and the
                    Employee and no person or entity will be regarded as a
                    third-party beneficiary of this Agreement.

               e.   Counterparts. This Agreement may be executed simultaneously
                    in two or more counterparts, each of which shall be deemed
                    an original.

               f.   Headings and Captions. The headings and captions used in
                    this Agreement are for ease of reference only and in no way
                    modify, or affect the meaning or construction of any of the
                    terms or provisions hereof.

               g.   Amendment; Waiver. This Agreement may be amended, modified,
                    superseded or canceled, and any of the terms may be waived,
                    only by a written instrument executed by each party or, in
                    the case of waiver, by the party or parties waiving
                    compliance. The delay or failure of either party at any time
                    or times to require performance of any provisions shall in
                    no manner affect the rights at a later time to enforce the
                    same. No waiver by either party of any condition or of the
                    breach of any term contained in this Agreement, whether by
                    conduct, or otherwise, in any one or more instances, shall
                    be deemed to be, or considered as, a further or continuing
                    waiver of any such condition or of the breach of such term
                    or any other term of this Agreement.

               h.   Governing Law. This Agreement and the rights and obligations
                    of the parties hereunder will be construed in accordance
                    with and governed by the laws of the Commonwealth of
                    Massachusetts, without giving effect to the conflict of law
                    principles thereof. Further, by accepting executing this
                    Agreement the Employee agrees that any action, demand, claim
                    or counterclaim in connection with any aspect of the
                    Employee's employment with the Company, or any separation of
                    employment (whether voluntary or involuntary) from the
                    Company, shall be resolved by a judge alone, and the
                    Employee waives and forever renounces the Employee's right
                    to a trial before a civil jury.

               i.   Interpretation. The parties acknowledge and agree that: (i)
                    each party and its counsel reviewed and negotiated the terms
                    and provisions of this Agreement and have contributed to its
                    revision; (ii) the rule of construction to the effect that
                    any ambiguities are resolved against the drafting party
                    shall not be employed in the interpretation of this
                    Agreement; and (iii) the terms and provisions of this
                    Agreement shall be construed fairly as to all parties hereto
                    and not in a favor of or against any party, regardless of
                    which party was generally responsible for the preparation of
                    this Agreement.


                                        5

<PAGE>

If you are in agreement with the foregoing, please sign where indicated below,
whereupon this Agreement shall become effective as of the Effective Date.

JOHN DUNCAN HIGGONS                     ARCHEMIX CORP.


By: /s/ John Duncan Higgons             By: /s/ Errol De Souza
    ---------------------------------       ------------------------------------
Print Name: JOHN DUNCAN HIGGONS         Print Name: Errol De Souza
                                        Title: President and Chief Executive
                                               Officer
Date: 12.15.05                          Date: 1/03/06


                                        6