| 22. Round | 17/02/2007 | FC St. Pauli | - | VfB Lübeck | 2:0 | ||||
| 21. Round | 21/02/2007 | Borussia Dortmund II | - | FC St. Pauli | 0:1 | ||||
| 24. Round | 03/03/2007 | FC St. Pauli | - | Hertha BSC II | 3:0 | ||||
| 25. Round | 10/03/2007 | 1. FC Union Berlin | - | FC St. Pauli | 2:0 | ||||
| 26. Round | 16/03/2007 | FC St. Pauli | - | SV Wilhelmshaven | 2:0 | ||||
| 27. Round | 24/03/2007 | Bayer Leverkusen II | - | FC St. Pauli | 2:1 | ||||
| 30. Round | 04/04/2007 | Hamburger SV II | - | FC St. Pauli | 0:0 | ||||
| 31. Round | 14/04/2007 | FC St. Pauli | - | Holstein Kiel | 2:0 |  |
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| 32. Round | 21/04/2007 | Bor. Mönchengladbach II | - | FC St. Pauli | 1:5 | |
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| 23. Round | 24/04/2007 | Werder Bremen II | - | FC St. Pauli | 0:2 | |
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| 33. Round | 27/04/2007 | FC St. Pauli | - | Rot Weiss Ahlen | 3:0 |  |
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| 35. Round | 12/05/2007 | FC St. Pauli | - | Fortuna Düsseldorf | 2:0 | ||||
| 36. Round | 20/05/2007 | Rot-Weiß Erfurt | - | FC St. Pauli | 0:3 | |
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| 37. Round | 25/05/2007 | FC St. Pauli | - | Dynamo Dresden | 2:2 | ||||
| 38. Round | 02/06/2007 | 1. FC Magdeburg | - | FC St. Pauli | 1:1 | |
Germany