| 5. Round | 16/09/2012 | FC St. Pauli [Youth] | - | VfL Osnabrück [Youth] | 1:1 | ||||
| 6. Round | 23/09/2012 | VfL Wolfsburg [Youth] | - | FC St. Pauli [Youth] | 2:1 |  |
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| 7. Round | 30/09/2012 | FC St. Pauli [Youth] | - | Hansa Rostock [Youth] | 3:0 | ||||
| 12. Round | 24/11/2012 | FC St. Pauli [Youth] | - | Holstein Kiel [Youth] | 1:1 | ||||
| 21. Round | 07/04/2013 | FC St. Pauli [Youth] | - | Energie Cottbus [Youth] | 1:0 | ||||
| 22. Round | 14/04/2013 | FC St. Pauli [Youth] | - | Chemnitzer FC [Youth] | 1:0 | ||||
| 23. Round | 21/04/2013 | Hannover 96 [Youth] | - | FC St. Pauli [Youth] | 3:2 | ||||
| 24. Round | 27/04/2013 | FC St. Pauli [Youth] | - | Hamburger SV [Youth] | 1:0 | |
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| 20. Round | 02/05/2013 | Hansa Rostock [Youth] | - | FC St. Pauli [Youth] | 2:1 | ||||
| 25. Round | 05/05/2013 | Holstein Kiel [Youth] | - | FC St. Pauli [Youth] | 3:2 | ||||
| 26. Round | 12/05/2013 | FC St. Pauli [Youth] | - | Hertha BSC [Youth] | 0:0 |
Germany