| 1. Round | 16/08/2008 | Hertha Zehlendorf [Youth B] | - | FC St. Pauli [Youth B] | 0:1 | ||||
| 2. Round | 23/08/2008 | FC St. Pauli [Youth B] | - | Hansa Rostock [Youth B] | 0:1 | ||||
| 3. Round | 30/08/2008 | Hertha BSC [Youth B] | - | FC St. Pauli [Youth B] | 6:2 | ||||
| 21. Round | 06/09/2008 | TeBe Berlin [Youth B] | - | FC St. Pauli [Youth B] | 2:1 | ||||
| 4. Round | 14/09/2008 | FC St. Pauli [Youth B] | - | Hamburger SV [Youth B] | 0:0 | ||||
| 5. Round | 27/09/2008 | VfL Osnabrück [Youth B] | - | FC St. Pauli [Youth B] | 2:1 | ||||
| 6. Round | 04/10/2008 | FC St. Pauli [Youth B] | - | Rot-Weiß Erfurt [Youth B] | 1:1 |  |
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| 14. Round | 12/10/2008 | FC St. Pauli [Youth B] | - | Hertha Zehlendorf [Youth B] | 1:2 | ||||
| 7. Round | 26/10/2008 | Werder Bremen [Youth B] | - | FC St. Pauli [Youth B] | 4:2 | ||||
| 13. Round | 14/12/2008 | FC St. Pauli [Youth B] | - | Concordia Hamburg [Youth B] | 5:0 | |
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| 18. Round | 15/03/2009 | FC St. Pauli [Youth B] | - | VfL Osnabrück [Youth B] | 0:3 |
Germany