| 1. Ronde | 17.08.2008 | FC St. Pauli [A-jun] | - | Eintracht Braunschweig [A-jun] | 0:4 | ||||
| 2. Ronde | 23.08.2008 | Werder Bremen [A-jun] | - | FC St. Pauli [A-jun] | 1:0 | ||||
| 3. Ronde | 30.08.2008 | FC St. Pauli [A-jun] | - | 1. FC Union Berlin [A-jun] | 2:2 | ||||
| 4. Ronde | 14.09.2008 | Chemnitzer FC [A-jun] | - | FC St. Pauli [A-jun] | 1:2 | ||||
| 5. Ronde | 28.09.2008 | FC St. Pauli [A-jun] | - | Hansa Rostock [A-jun] | 0:3 | ||||
| 6. Ronde | 04.10.2008 | Hannover 96 [A-jun] | - | FC St. Pauli [A-jun] | 6:1 | ||||
| 7. Ronde | 26.10.2008 | FC St. Pauli [A-jun] | - | Hertha BSC [A-jun] | 1:4 | ||||
| 8. Ronde | 01.11.2008 | Energie Cottbus [A-jun] | - | FC St. Pauli [A-jun] | 1:0 | ||||
| 9. Ronde | 09.11.2008 | FC St. Pauli [A-jun] | - | Hamburger SV [A-jun] | 1:6 | ||||
| 10. Ronde | 16.11.2008 | VfL Osnabrück [A-jun] | - | FC St. Pauli [A-jun] | 2:2 | ||||
| 11. Ronde | 29.11.2008 | FC St. Pauli [A-jun] | - | FC Carl Zeiss Jena [A-jun] | 4:0 | ||||
| 12. Ronde | 07.12.2008 | FC St. Pauli [A-jun] | - | VfL Wolfsburg [A-jun] | 1:4 | ||||
| 18. Ronde | 14.03.2009 | Hansa Rostock [A-jun] | - | FC St. Pauli [A-jun] | 4:0 |
Duitsland