| 3. Round | 14/09/2003 | FV Dresden-Nord [Youth] | - | FC St. Pauli [Youth] | 3:1 | ||||
| 4. Round | 20/09/2003 | FC St. Pauli [Youth] | - | Hamburger SV [Youth] | 2:0 | ||||
| 5. Round | 28/09/2003 | Bremen 1860 [Youth] | - | FC St. Pauli [Youth] | 0:2 | ||||
| 12. Round | 06/12/2003 | Werder Bremen [Youth] | - | FC St. Pauli [Youth] | 5:0 | ||||
| 14. Round | 21/02/2004 | FC St. Pauli [Youth] | - | VfL Wolfsburg [Youth] | 3:1 | ||||
| 15. Round | 28/02/2004 | Tasmania Gropiusstadt [Youth] | - | FC St. Pauli [Youth] | 0:2 | ||||
| 16. Round | 07/03/2004 | FC St. Pauli [Youth] | - | FV Dresden-Nord [Youth] | 0:4 |  |
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| 17. Round | 13/03/2004 | Hamburger SV [Youth] | - | FC St. Pauli [Youth] | 1:0 | ||||
| 18. Round | 20/03/2004 | FC St. Pauli [Youth] | - | Bremen 1860 [Youth] | 7:1 | ||||
| 19. Round | 03/04/2004 | Hannover 96 [Youth] | - | FC St. Pauli [Youth] | 3:1 | ||||
| 23. Round | 09/05/2004 | Hansa Rostock [Youth] | - | FC St. Pauli [Youth] | 4:0 | ||||
| 24. Round | 15/05/2004 | VfL Osnabrück [Youth] | - | FC St. Pauli [Youth] | 1:4 |
Germany