| 1. Round | 17/08/2008 | FC St. Pauli [Youth] | - | Eintracht Braunschweig [Youth] | 0:4 | ||||
| 2. Round | 23/08/2008 | Werder Bremen [Youth] | - | FC St. Pauli [Youth] | 1:0 | ||||
| 3. Round | 30/08/2008 | FC St. Pauli [Youth] | - | 1. FC Union Berlin [Youth] | 2:2 |  |
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| 4. Round | 14/09/2008 | Chemnitzer FC [Youth] | - | FC St. Pauli [Youth] | 1:2 | ||||
| 5. Round | 28/09/2008 | FC St. Pauli [Youth] | - | Hansa Rostock [Youth] | 0:3 | ||||
| 6. Round | 04/10/2008 | Hannover 96 [Youth] | - | FC St. Pauli [Youth] | 6:1 | |
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| 7. Round | 26/10/2008 | FC St. Pauli [Youth] | - | Hertha BSC [Youth] | 1:4 | |
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| 8. Round | 01/11/2008 | Energie Cottbus [Youth] | - | FC St. Pauli [Youth] | 1:0 | ||||
| 9. Round | 09/11/2008 | FC St. Pauli [Youth] | - | Hamburger SV [Youth] | 1:6 | ||||
| 10. Round | 16/11/2008 | VfL Osnabrück [Youth] | - | FC St. Pauli [Youth] | 2:2 | ||||
| 11. Round | 29/11/2008 | FC St. Pauli [Youth] | - | FC Carl Zeiss Jena [Youth] | 4:0 | |
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| 12. Round | 07/12/2008 | FC St. Pauli [Youth] | - | VfL Wolfsburg [Youth] | 1:4 | |
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| 16. Round | 01/03/2009 | 1. FC Union Berlin [Youth] | - | FC St. Pauli [Youth] | 0:0 |
Germany