UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549

FORM 40-F

[Check One]

|o |  | Registration Statement Pursuant to Section 12 of the
Securities Exchange Act of 1934   
|- |  | ---------------------------------------------------------------------------------------
|ý |  | Annual Report Pursuant to Section 13(a) or 15(d) of the
Securities Exchange Act of 1934

|For the fiscal year ended: |  | September 30, 2003 |  | Commission File Number: |  | 
|-------------------------- |  | ------------------ |  | ----------------------- |  | 

|Axcan Pharma Inc.                                                                                                        
|-------------------------------------------------------------------------------------------------------------------------
|(Exact name of Registrant as specified in its charter)                                                                   
|N/A                                                                                                                      
|(Translation of Registrant's name into English (if applicable))                                                          
|Canada                                                                                                                   
|(Province or other jurisdiction of incorporation or organization)                                                        
|5122                                                                                                                     
|(Primary Standard Industrial Classification Code Number (if applicable))                                                 
|N/A                                                                                                                      
|(I.R.S. Employer Identification Number (if applicable))                                                                  
|597 Laurier Blvd., Mont St-Hilaire, Quebec, Canada J3H 6C4 (450) 467-5138                                                
|(Address and telephone number of Registrant's principal executive offices)                                               
|CT Corporation System, 111 8th Avenue, 15th Floor, New York, New York 10011 (212) 894-8700                               
|(Name, address (including zip code) and telephone number)
(including area code of agent for service in the United States)

Securities
registered or to be registered pursuant to Section 12(b) of the Act.

|Title of each class                                                             |  | Name of each exchange on which registered
|------------------------------------------------------------------------------- |  | -----------------------------------------
|                                                                                |  |                                          
|None                                                                            |  |                                          
|                                                                                |  |                                          
|Securities registered or to be registered pursuant to Section 12(g) of the Act.

|Common Shares                                                                             
|------------------------------------------------------------------------------------------
|(Title of Class)                                                                          
|Securities for which there is a reporting obligation pursuant to Section 15(d) of the Act.
|Common Shares                                                                             
|(Title of Class)                                                                          

---

For
annual reports, indicate by check mark the information filed with this Form:

|                                                                                                                                                                                                                                                                                                                                                              |  | o |  | Annual information form |  | ý |  | Audited annual financial statements
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | - |  | ----------------------- |  | - |  | -----------------------------------
|Indicate the number of outstanding shares of each of the issuer's classes of capital or common stock as of the close of the period covered by the annual
report.                                                                                                                                                                                             
|Common Shares              45,004,320                                                                                                                                                                                                                                                                                                                        
|Indicate by check mark whether the Registrant by filing the information contained in this Form is also thereby furnishing the information to the Commission
pursuant to Rule 12g3-2(b) under the Securities Exchange Act of 1934 (the"Exchange Act"). If "Yes" is marked, indicate the filing number assigned to the Registrant in connection with such
Rule.

|                                                                                                                                                                                                                                                                                                                                     |  | Yes |  | o |  | No |  | ý
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |  | --- |  | - |  | -- |  | -
|Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Exchange Act during
the preceding 12 months (or for such shorter period that the Registrant was required to file such reports) and (2) has been subject to such filing requirements for the past 90 days.
|                                                                                                                                                                                                                                                                                                                                     |  | Yes |  | ý |  | No |  | o

**********

Registrant
undertakes to make available, in person or by telephone, representatives to respond to inquiries made by the Commission staff, and to furnish promptly, when requested to do so
by the Commission staff, information relating to: the securities registered pursuant to Form 40-F; the securities in relation to which the obligation to file an annual report on
Form 40-F arises; or transactions in said securities.

SIGNATURES

Pursuant to the requirements of the Exchange Act, the Registrant certifies that it meets all of the requirements for filing on Form 40-F
and has duly caused this annual report to be signed on its behalf by the undersigned, thereto duly authorized.

|                       |  | AXCAN PHARMA INC.(Registrant)
|---------------------- |  | -----------------------------
|Date: January 23, 2004 |  | By:                          

---

EXHIBITS

99.1

Additional disclosures required pursuant to Form 40-F instructions.99.2

Management's Discussion and Analysis
 Pages 16 - 27 of Axcan's 2003 Annual Report99.3

Consolidated Financial Statements, U.S. GAAP
 Pages 29 - 58 of Axcan's 2003 Annual Report99.4

Consolidated Financial Statements, Canadian GAAP
 Pages 59 - 85 of Axcan's 2003 Annual Report99.5

Rule 13a-14(a) Certificate99.6

Rule 13a-14(a) Certificate99.7

Certification Pursuant to 18 U.S.C. Section 135099.8

Certification Pursuant to 18 U.S.C. Section 135099.9

Consent of Independent Public Accountants


---

QuickLinks