| 1. Round | 04/08/2012 | FC St. Pauli II | - | BV Cloppenburg | 4:2 |  |
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| 2. Round | 11/08/2012 | VfB Oldenburg | - | FC St. Pauli II | 1:2 | ||||
| 4. Round | 26/08/2012 | Schwarz-Weiß Rehden | - | FC St. Pauli II | 1:1 | ||||
| 5. Round | 28/08/2012 | Werder Bremen II | - | FC St. Pauli II | 6:0 | ||||
| 6. Round | 06/09/2012 | FC St. Pauli II | - | VfB Lübeck | annull. |  |
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| 7. Round | 14/09/2012 | VfL Wolfsburg II | - | FC St. Pauli II | 3:0 | ||||
| 8. Round | 22/09/2012 | FC St. Pauli II | - | Goslarer SC | 1:4 | ||||
| 9. Round | 28/09/2012 | Holstein Kiel | - | FC St. Pauli II | 6:0 | |
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| 3. Round | 03/10/2012 | FC St. Pauli II | - | SV Wilhelmshaven | 2:3 | ||||
| 11. Round | 13/10/2012 | FC Oberneuland | - | FC St. Pauli II | annull. | ||||
| 12. Round | 21/10/2012 | FC St. Pauli II | - | Hamburger SV II | 1:1 | |
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| 13. Round | 24/10/2012 | Victoria Hamburg | - | FC St. Pauli II | 0:0 | ||||
| 10. Round | 30/10/2012 | FC St. Pauli II | - | SV Meppen | 0:4 | ||||
| 14. Round | 04/11/2012 | FC St. Pauli II | - | ETSV Weiche Flensburg | 1:2 | |
Germany