| 3. Round | 23/08/2011 | VfB Lübeck | - | FC St. Pauli II | 5:1 |  |
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| 4. Round | 28/08/2011 | FC St. Pauli II | - | 1. FC Magdeburg | 0:2 |  |
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| 12. Round | 06/11/2011 | Berliner AK 07 | - | FC St. Pauli II | 2:3 | ||||
| 13. Round | 13/11/2011 | FC St. Pauli II | - | Germania Halberstadt | 0:0 | ||||
| 14. Round | 18/11/2011 | VfL Wolfsburg II | - | FC St. Pauli II | 2:2 | ||||
| 15. Round | 30/11/2011 | FC St. Pauli II | - | Hallescher FC | 2:2 | ||||
| 16. Round | 03/12/2011 | SV Meppen | - | FC St. Pauli II | 1:0 | ||||
| 20. Round | 17/02/2012 | FC St. Pauli II | - | VfB Lübeck | 1:3 | ||||
| 21. Round | 26/02/2012 | 1. FC Magdeburg | - | FC St. Pauli II | 2:2 | ||||
| 19. Round | 07/03/2012 | TSV Havelse | - | FC St. Pauli II | 3:2 | ||||
| 23. Round | 11/03/2012 | VFC Plauen | - | FC St. Pauli II | 4:1 | |
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| 24. Round | 17/03/2012 | FC St. Pauli II | - | Energie Cottbus II | 3:1 |  |
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| 25. Round | 24/03/2012 | Hannover 96 II | - | FC St. Pauli II | 3:0 | |
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| 26. Round | 31/03/2012 | ZFC Meuselwitz | - | FC St. Pauli II | 1:1 | ||||
| 17. Round | 04/04/2012 | FC St. Pauli II | - | Hamburger SV II | 1:0 | ||||
| 27. Round | 08/04/2012 | FC St. Pauli II | - | RB Leipzig | 1:2 | |
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| 28. Round | 11/04/2012 | Holstein Kiel | - | FC St. Pauli II | 4:0 |
Germany