| 11. Round | 25/10/2008 | 1. FC Union Berlin | - | SC Paderborn 07 | 3:2 | ||||
| 16. Round | 22/11/2008 | SC Paderborn 07 | - | VfR Aalen | 4:0 | ||||
| 19. Round | 13/12/2008 | SC Paderborn 07 | - | Stuttgarter Kickers | 2:0 | ||||
| 20. Round | 20/12/2008 | SC Paderborn 07 | - | Fortuna Düsseldorf | 0:0 | ||||
| 21. Round | 08/02/2009 | SpVgg Unterhaching | - | SC Paderborn 07 | 2:1 |  |
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| 22. Round | 14/02/2009 | SC Paderborn 07 | - | SV Sandhausen | 1:2 | ||||
| 25. Round | 07/03/2009 | Rot-Weiß Erfurt | - | SC Paderborn 07 | 1:4 | ||||
| 26. Round | 15/03/2009 | SC Paderborn 07 | - | Kickers Emden | 2:0 | ||||
| 23. Round | 18/03/2009 | Jahn Regensburg | - | SC Paderborn 07 | 0:4 | ||||
| 27. Round | 22/03/2009 | Bayern München II | - | SC Paderborn 07 | 2:1 | ||||
| 32. Round | 18/04/2009 | SC Paderborn 07 | - | Dynamo Dresden | 1:2 | ||||
| 34. Round | 02/05/2009 | SC Paderborn 07 | - | FC Carl Zeiss Jena | 2:0 | |
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| 35. Round | 09/05/2009 | VfR Aalen | - | SC Paderborn 07 | 3:3 | ||||
| 37. Round | 16/05/2009 | SC Paderborn 07 | - | Wacker Burghausen | 6:0 |
Germany