| 2. Round | 09/08/2003 | FC St. Pauli | - | Preußen Münster | 1:1 | ||||
| 3. Round | 17/08/2003 | FC St. Pauli | - | Dynamo Dresden | 2:2 | ||||
| 4. Round | 23/08/2003 | Wuppertaler SV | - | FC St. Pauli | 3:0 |  |
|||
| 5. Round | 26/08/2003 | FC St. Pauli | - | Hamburger SV II | 3:0 |  |
|
||
| 6. Round | 06/09/2003 | Holstein Kiel | - | FC St. Pauli | 0:5 | ||||
| 7. Round | 13/09/2003 | FC St. Pauli | - | Rot-Weiss Essen | 1:2 | |
|||
| 8. Round | 20/09/2003 | Chemnitzer FC | - | FC St. Pauli | 1:2 | |
|||
| 9. Round | 27/09/2003 | FC St. Pauli | - | SC Paderborn 07 | 2:0 | ||||
| 11. Round | 10/10/2003 | FC St. Pauli | - | Borussia Dortmund II | 1:1 |  |
|||
| 12. Round | 19/10/2003 | Sachsen Leipzig | - | FC St. Pauli | 2:1 | ||||
| 15. Round | 07/11/2003 | FC St. Pauli | - | VfR Neumünster | 1:1 | |
|||
| 17. Round | 22/11/2003 | FC St. Pauli | - | Eintracht Braunschweig | 1:0 | ||||
| 18. Round | 28/11/2003 | FC St. Pauli | - | SG Wattenscheid 09 | 2:2 | |
|||
| 19. Round | 06/12/2003 | Preußen Münster | - | FC St. Pauli | 2:0 |
USA