| 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 | ||||
| 14. Round | 12/10/2008 | FC St. Pauli [Youth B] | - | Hertha Zehlendorf [Youth B] | 1:2 |  |
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| 7. Round | 26/10/2008 | Werder Bremen [Youth B] | - | FC St. Pauli [Youth B] | 4:2 | ||||
| 8. Round | 01/11/2008 | FC St. Pauli [Youth B] | - | TeBe Berlin [Youth B] | 0:2 | ||||
| 9. Round | 09/11/2008 | Hannover 96 [Youth B] | - | FC St. Pauli [Youth B] | 0:3 | ||||
| 10. Round | 15/11/2008 | FC St. Pauli [Youth B] | - | Energie Cottbus [Youth B] | 0:1 | ||||
| 11. Round | 30/11/2008 | Holstein Kiel [Youth B] | - | FC St. Pauli [Youth B] | 0:0 | ||||
| 16. Round | 01/03/2009 | FC St. Pauli [Youth B] | - | Hertha BSC [Youth B] | 2:1 | ||||
| 18. Round | 15/03/2009 | FC St. Pauli [Youth B] | - | VfL Osnabrück [Youth B] | 0:3 | ||||
| 19. Round | 22/03/2009 | Rot-Weiß Erfurt [Youth B] | - | FC St. Pauli [Youth B] | 1:2 | ||||
| 20. Round | 05/04/2009 | FC St. Pauli [Youth B] | - | Werder Bremen [Youth B] | 1:8 |  |
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| 22. Round | 26/04/2009 | FC St. Pauli [Youth B] | - | Hannover 96 [Youth B] | 2:1 |
Germany