| 2. Round | 20/08/2006 | SC Paderborn 07 | - | FC Augsburg | 1:0 | ||||
| 4. Round | 17/09/2006 | SC Paderborn 07 | - | Kickers Offenbach | 2:1 | ||||
| 5. Round | 24/09/2006 | FC Carl Zeiss Jena | - | SC Paderborn 07 | 1:1 |  |
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| 6. Round | 29/09/2006 | SC Paderborn 07 | - | 1. FC Köln | 2:0 | ||||
| 7. Round | 15/10/2006 | SC Paderborn 07 | - | TuS Koblenz | 1:2 | ||||
| 10. Round | 03/11/2006 | Karlsruher SC | - | SC Paderborn 07 | 3:0 | ||||
| 13. Round | 19/11/2006 | SC Paderborn 07 | - | SpVgg Greuther Fürth | 0:0 | ||||
| 14. Round | 26/11/2006 | Erzgebirge Aue | - | SC Paderborn 07 | 1:0 | ||||
| 15. Round | 01/12/2006 | SC Paderborn 07 | - | SC Freiburg | 1:1 | ||||
| 16. Round | 10/12/2006 | MSV Duisburg | - | SC Paderborn 07 | 1:1 | ||||
| 17. Round | 17/12/2006 | SC Paderborn 07 | - | Wacker Burghausen | 1:1 | ||||
| 30. Round | 22/04/2007 | SpVgg Greuther Fürth | - | SC Paderborn 07 | 3:0 | ||||
| 32. Round | 04/05/2007 | SC Freiburg | - | SC Paderborn 07 | 0:1 | ||||
| 34. Round | 20/05/2007 | Wacker Burghausen | - | SC Paderborn 07 | 5:1 |
Belgium