<PAGE>   1
                                                                    Exhibit 10.3




                                 PROMISSORY NOTE
                                 ---------------


$9,000,000.00                                              Boston, Massachusetts
                                                              September 24, 1998


         FOR VALUE RECEIVED, the undersigned Alkermes, Inc., a Pennsylvania
corporation ("Alkermes"), Alkermes Controlled Therapeutics, Inc., a Pennsylvania
corporation ("ACT I") and Alkermes Controlled Therapeutics Inc. II, a
Pennsylvania corporation ("ACT II") (Alkermes, ACT I and ACT II being referred
to herein individually as a "Borrower" and collectively as the "Borrowers")
hereby jointly and severally promise to pay to the order of FLEET NATIONAL BANK
(the "Bank") the principal amount of Nine Million and 00/100 ($9,000,000.00)
Dollars or such portion thereof as may be advanced under Section 2(a) of the
below-described Loan Supplement and Modification Agreement ("Principal"), with
interest, at the rate hereinafter set forth, on the daily balance of all unpaid
Principal, from the date hereof until payment in full of all Principal and
interest hereunder. As used herein, (i) "Loan Supplement and Modification
Agreement" means that certain Third Loan Supplement and Modification Agreement
of even date herewith among the Borrowers and the Bank and (ii) "Letter
Agreement" means that certain letter agreement dated September 27, 1996 among
the Borrowers and the Bank, as amended.

         Interest on all unpaid Principal shall be due and payable monthly in
arrears, on the first Business Day (as defined in the Loan Supplement and
Modification Agreement) of each month, commencing on the first such date after
the advance of any Principal and continuing on the first Business Day of each
month thereafter and on the date of payment of this note in full, at a
fluctuating rate per annum (computed on the basis of a year of three hundred
sixty (360) days for the actual number of days elapsed) which shall at all times
(except as provided in the next following sentence) be equal to the Prime Rate,
as in effect from time to time (but in no event in excess of the maximum rate
permitted by then applicable law), with a change in the aforesaid rate of
interest to become effective on the same day on which any change in the Prime
Rate is effective; provided, however, that (A) if a LIBOR Interest Rate (as
defined in the Loan Supplement and Modification Agreement) shall have become
applicable to all or any portion of the outstanding Principal for any Interest
Period (as defined in the Loan Supplement and Modification Agreement), then
interest on such Principal or portion thereof shall accrue at said applicable
LIBOR Interest Rate for such Interest Period and shall be payable on the
Interest Payment Date (as defined in the Loan Supplement and Modification
Agreement) applicable to such Interest Period, and (B) if a COF Interest Rate
(as defined in the Loan Supplement and Modification Agreement) shall be
applicable to all or any portion of the outstanding Principal, then interest on
such outstanding Principal or portion thereof shall accrue at said COF Interest
Rate and shall be paid on the first Business Day of each month. Overdue
Principal and, to the extent permitted by law, overdue interest shall bear
interest at a fluctuating rate per annum which at all times shall be equal to
the sum of (i) four (4%) percent per annum PLUS (ii) the per annum rate
otherwise payable under this note with respect to the Principal which is overdue
(or as to which such interest is overdue) (but in no event in excess of the
maximum rate permitted by then applicable law), compounded monthly and payable
on demand. As used herein, "Prime Rate" 










<PAGE>   2

means that variable rate of interest per annum designated by the Bank from time
to time as its prime rate, it being understood that such rate is merely a
reference rate and does not necessarily represent the lowest or best rate being
charged to any customer. If the entire amount of any required Principal and/or
interest is not paid within ten (10) days after the same is due, the Borrowers
shall pay (and shall be jointly and severally obligated to pay) to the Bank a
late fee equal to five percent (5%) of the required payment.

         The Principal of this note represents the Tranche A September 1998 Term
Loans (as defined in the Loan Supplement and Modification Agreement) made
pursuant to Section 2(a) of the Loan Supplement and Modification Agreement. The
Principal of this note shall be repaid by the Borrowers in seventeen (17) equal
consecutive quarterly installments (each in an amount equal to 1/18th of the
aggregate principal amount of the Tranche A September 1998 Term Loans
outstanding at the close of business on March 31, 1999), such installments to
commence on June 30, 1999 and to continue on the last Business Day of each
calendar quarter thereafter through and including June 30, 2003, PLUS an
eighteenth (18th) and final installment payment due on September 30, 2003 in an
amount equal to all then unpaid Principal and all interest accrued but unpaid
thereon. The Borrowers may at any time and from time to time prepay all or any
portion of Principal, but, as to Fixed Rate Loans (as defined in the Loan
Supplement and Modification Agreement), only at the times and in the manner, and
(under certain circumstances) with the additional payments, provided for in the
Loan Supplement and Modification Agreement. Any prepayment of Principal, in
whole or in part, will be without premium or penalty (but, in the case of Fixed
Rate Loans, may require payment of additional amounts, as provided for in the
Loan Supplement and Modification Agreement). Each Principal prepayment shall be
accompanied by payment of all interest on the prepaid amount accrued but unpaid
to the date of payment. Any partial prepayment of Principal shall be applied
against Principal installments (including the final installment payment of
Principal) thereafter coming due, in inverse order of normal maturity.

         Payments of both Principal and interest shall be made, in lawful money
of the United States in immediately available funds, at the office of the Bank
located at One Federal Street, Boston, Massachusetts 02110, or at such other
address as the Bank may from time to time designate.

         Each of the undersigned Borrowers irrevocably authorizes the Bank to
make or cause to be made, on a schedule attached to this note or on the books of
the Bank, at or following the time of receiving any payment of Principal, an
appropriate notation reflecting such transaction and the then aggregate unpaid
balance of Principal. Failure of the Bank to make any such notation shall not,
however, affect any obligation of any Borrower hereunder or under the Letter
Agreement. The Principal balance of this note, as recorded by the Bank from time
to time on such schedule or on such books, shall constitute presumptive evidence
of the unpaid principal amount of the Tranche A September 1998 Term Loans.

         Each Borrower hereby (a) waives notice of and consents to any and all
advances, settlements, compromises, favors and indulgences (including, without
limitation, any extension or postponement of the time for payment), any and all
receipts, substitutions, additions, exchanges and releases of collateral, and
any and all additions, substitutions and releases of any 



                                      -2-



<PAGE>   3

person primarily or secondarily liable, (b) waives presentment, demand, notice,
protest and all other demands and notices generally in connection with the
delivery, acceptance, performance, default or enforcement of or under this note,
and (c) agrees to pay, to the extent permitted by law, all reasonable costs and
expenses, including, without limitation, reasonable attorneys' fees, incurred or
paid by the Bank in enforcing this note and any collateral or security therefor,
all whether or not litigation is commenced.

         This note is secured, INTER ALIA, by a Security Agreement dated as of
September 27, 1996, as amended (as so amended, the "Security Agreement") given
by the Borrowers to the Bank. This note is the "Tranche A September 1998 Term
Note" referred to in the Loan Supplement and Modification Agreement and
constitutes an "Additional Term Note" as defined in the Letter Agreement and the
Security Agreement and is entitled to the benefits thereof. This note is subject
to prepayment under the conditions set forth in the Letter Agreement and the
Loan Supplement and Modification Agreement (which, in the case of Fixed Rate
Loans, may require the making of certain additional payments, as provided for in
the Loan Supplement and Modification Agreement). The maturity of this note may
be accelerated upon the occurrence of an Event of Default, as provided in the
Letter Agreement. This note is the joint and several obligation of the
Borrowers.

         EACH BORROWER HEREBY KNOWINGLY, VOLUNTARILY AND INTENTIONALLY WAIVES
THE RIGHT TO A TRIAL BY JURY IN RESPECT OF ANY CLAIM BASED ON THIS NOTE OR
ARISING OUT OF, UNDER OR IN CONNECTION WITH THIS NOTE OR ANY RELATED DOCUMENTS
OR OUT OF ANY COURSE OF CONDUCT, COURSE OF DEALING, STATEMENTS (WHETHER ORAL OR
WRITTEN) OR ACTIONS OF ANY PERSON. THIS WAIVER CONSTITUTES A MATERIAL INDUCEMENT
FOR THE BANK TO ACCEPT THIS NOTE AND TO MAKE LOANS AS CONTEMPLATED IN THE LETTER
AGREEMENT AND THE LOAN SUPPLEMENT AND MODIFICATION AGREEMENT.

         Executed, as an instrument under seal, as of the day and year first
above written.


CORPORATE SEAL                               ALKERMES, INC.

ATTEST:

                                             By: /s/ Robert A. Breyer
/s/ Patricia L. Allen                            -------------------------------
---------------------------------                Name: Robert A. Breyer
Assistant Secretary                              Title: President



                                      -3-




<PAGE>   4

CORPORATE SEAL                               ALKERMES CONTROLLED
                                               THERAPEUTICS, INC.
ATTEST:

                                             By: /s/ Robert A. Breyer
/s/ Patricia L. Allen                            -------------------------------
---------------------------------                Name: Robert A. Breyer
Assistant Secretary                              Title: Vice President



CORPORATE SEAL                               ALKERMES CONTROLLED
                                               THERAPEUTICS INC. II
ATTEST:

                                             By: /s/ Robert A. Breyer
/s/ Patricia L. Allen                            -------------------------------
---------------------------------                Name: Robert A. Breyer
Assistant Secretary                              Title: Vice President






                                      -4-