| 1. Round | 16/07/2011 | FC St. Pauli | - | FC Ingolstadt 04 | 2:0 | ||||
| 4. Round | 12/08/2011 | VfL Bochum | - | FC St. Pauli | 1:2 | ||||
| 5. Round | 22/08/2011 | FC St. Pauli | - | MSV Duisburg | 2:1 | ||||
| 6. Round | 28/08/2011 | Eintracht Braunschweig | - | FC St. Pauli | 1:0 | ||||
| 8. Round | 19/09/2011 | Karlsruher SC | - | FC St. Pauli | 0:2 | ||||
| 10. Round | 01/10/2011 | Energie Cottbus | - | FC St. Pauli | 1:4 | ||||
| 12. Round | 23/10/2011 | FC St. Pauli | - | FSV Frankfurt | 2:1 | ||||
| 13. Round | 28/10/2011 | 1. FC Union Berlin | - | FC St. Pauli | 0:2 | ||||
| 14. Round | 05/11/2011 | FC St. Pauli | - | SpVgg Greuther Fürth | 2:2 | ||||
| 15. Round | 19/11/2011 | Hansa Rostock | - | FC St. Pauli | 1:3 | ||||
| 16. Round | 27/11/2011 | FC St. Pauli | - | Dynamo Dresden | 3:1 | ||||
| 19. Round | 19/12/2011 | FC St. Pauli | - | Eintracht Frankfurt | 2:0 |  |
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| 20. Round | 04/02/2012 | Alemannia Aachen | - | FC St. Pauli | 2:1 |  |
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| 28. Round | 02/04/2012 | Fortuna Düsseldorf | - | FC St. Pauli | 0:0 | ||||
| 29. Round | 07/04/2012 | FSV Frankfurt | - | FC St. Pauli | 3:3 | ||||
| 30. Round | 10/04/2012 | FC St. Pauli | - | 1. FC Union Berlin | 2:1 | ||||
| 31. Round | 13/04/2012 | SpVgg Greuther Fürth | - | FC St. Pauli | 2:1 |
Germany