| 4. Round | 28/08/2011 | FC St. Pauli II | - | 1. FC Magdeburg | 0:2 | ||||
| 2. Round | 03/09/2011 | FC St. Pauli II | - | TSV Havelse | 2:1 | ||||
| 7. Round | 25/09/2011 | Energie Cottbus II | - | FC St. Pauli II | 1:2 | ||||
| 8. Round | 01/10/2011 | FC St. Pauli II | - | Hannover 96 II | 3:1 | ||||
| 23. Round | 11/03/2012 | VFC Plauen | - | FC St. Pauli II | 4:1 | ||||
| 24. Round | 17/03/2012 | FC St. Pauli II | - | Energie Cottbus II | 3:1 | ||||
| 17. Round | 04/04/2012 | FC St. Pauli II | - | Hamburger SV II | 1:0 | ||||
| 28. Round | 11/04/2012 | Holstein Kiel | - | FC St. Pauli II | 4:0 | ||||
| 29. Round | 14/04/2012 | FC St. Pauli II | - | Berliner AK 07 | 1:3 | ||||
| 34. Round | 18/04/2012 | Hamburger SV II | - | FC St. Pauli II | 0:0 | ||||
| 30. Round | 22/04/2012 | Germania Halberstadt | - | FC St. Pauli II | 4:1 | ||||
| 32. Round | 06/05/2012 | Hallescher FC | - | FC St. Pauli II | 5:0 | ||||
| 33. Round | 12/05/2012 | FC St. Pauli II | - | SV Meppen | 2:3 |
Germany