| 1. Round | 07/08/2005 | SpVgg Unterhaching | - | SC Paderborn 07 | 3:0 | ||||
| 2. Round | 14/08/2005 | SC Paderborn 07 | - | 1. FC Saarbrücken | 5:0 | ||||
| 7. Round | 25/09/2005 | Dynamo Dresden | - | SC Paderborn 07 | 0:2 | ||||
| 14. Round | 27/11/2005 | Alemannia Aachen | - | SC Paderborn 07 | 2:1 | ||||
| 20. Round | 05/02/2006 | SC Paderborn 07 | - | Energie Cottbus | 0:0 | ||||
| 21. Round | 12/02/2006 | LR Ahlen | - | SC Paderborn 07 | 0:2 | ||||
| 22. Round | 19/02/2006 | SC Paderborn 07 | - | Hansa Rostock | 3:0 | ||||
| 23. Round | 24/02/2006 | SpVgg Greuther Fürth | - | SC Paderborn 07 | 1:1 | ||||
| 25. Round | 10/03/2006 | Kickers Offenbach | - | SC Paderborn 07 | 1:1 | ||||
| 26. Round | 19/03/2006 | SC Paderborn 07 | - | TSV 1860 München | 0:1 | ||||
| 27. Round | 24/03/2006 | Eintracht Braunschweig | - | SC Paderborn 07 | 2:0 | ||||
| 28. Round | 31/03/2006 | SC Paderborn 07 | - | VfL Bochum | 1:3 | ||||
| 29. Round | 09/04/2006 | SC Freiburg | - | SC Paderborn 07 | 1:0 | ||||
| 33. Round | 07/05/2006 | SC Paderborn 07 | - | Erzgebirge Aue | 0:2 | ||||
| 34. Round | 14/05/2006 | Karlsruher SC | - | SC Paderborn 07 | 2:3 |
Serbia