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                                                                    EXHIBIT 10.9

                                           November 8, 2004


Joshua S. Boger
243 Old Pickard Road
Concord, MA 01742

Re:  Second Amendment to Employment Agreement

Dear Joshua,

       The Employment Agreement dated as of November 1, 1994, as amended by
letter agreement dated May 12, 1995, between you and Vertex Pharmaceuticals
Incorporated (the "Agreement") hereby is amended, effective November 8, 2004, by
deleting Section 6.4 in its entirety, and substituting the following:

       6.4  TERMINATION WITHOUT CAUSE. If the Executive's employment is
            terminated by the Company without Cause, the Executive shall be
            entitled to 18 months of Severance Pay. "Severance Pay" shall mean
            an amount equal to the Executive's base salary then in effect, plus
            the amount of the target bonus for the year in which the Executive's
            employment is terminated divided by twelve (12) (each of the 12
            shares to constitute a "month's" Severance Pay). In addition: (i)
            all unexercisable stock options held by the Executive as of the date
            of termination shall be deemed to have been held by the Executive
            for an additional eighteen (18) months after the date of
            termination, for purposes of vesting and exercise rights, and any
            unexercisable stock options that become exercisable as a result
            thereof shall remain exercisable until the earlier of (1) the end of
            the 90-day period following the date of termination and (2) the date
            the option would otherwise expire and (ii) the Company's lapsing
            repurchase right with respect to shares of restricted stock held by
            the Executive shall lapse with respect to the Pro-Rata Share of
            Restricted Stock. The "Pro-Rata Share of Restricted Stock" shall
            mean, for any grant of restricted stock as to which the Company's
            repurchase right lapses ratably over a specified period (e.g. in
            equal annual increments over four years), that number of shares as
            to which the Company's repurchase right with respect to those shares
            would have lapsed if the Executive's employment by the Company had
            continued an additional eighteen month period. For any other shares
            of restricted stock, "Pro-Rata Share of Restricted Stock" shall
            mean, as to any shares of restricted stock which were granted on the
            same date and as to which the Company's repurchase right lapses on
            the same date, that portion of such shares calculated by multiplying
            the number of shares by a fraction, the numerator of which is the
            number of days that have passed since the date of grant, plus the
            number of days in 18 months, and the denominator of which is the
            total number of days from the date of the grant until the date
            (without regard to



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Joshua S. Boger
November 8, 2004
Page 2


            any provisions for earlier vesting upon achievement of a specified
            goal) on which the Company's repurchase right would lapse under the
            terms of the grant. Notwithstanding the foregoing, the terms of any
            option agreement or restricted stock agreement shall govern the
            acceleration of vesting or lapsing of the Company's repurchase
            rights, as applicable, except to the extent that the terms of this
            Employment Agreement are more favorable to the Executive.

       As so amended, the Agreement shall remain in full force and effect.

       If you agree to the foregoing amendment, please so indicate by signing
and returning the enclosed copy of this letter.

                                         VERTEX PHARMACEUTICALS INCORPORATED



                                         By: /s/ VICKI L. SATO
                                            ------------------------------------
                                             Vicki L. Sato, President


Accepted and Agreed:


/s/ JOSHUA S. BOGER
- -----------------------------------
Joshua S. Boger