| 1. Round | 01/08/2003 | Borussia Dortmund II | - | SC Paderborn 07 | 0:1 | ||||
| 2. Round | 09/08/2003 | SC Paderborn 07 | - | Sachsen Leipzig | 2:1 | ||||
| 3. Round | 16/08/2003 | 1. FC Köln II | - | SC Paderborn 07 | 0:1 | ||||
| 4. Round | 22/08/2003 | SC Paderborn 07 | - | Werder Bremen II | 1:1 | ||||
| 5. Round | 30/08/2003 | VfR Neumünster | - | SC Paderborn 07 | 1:3 | ||||
| 6. Round | 06/09/2003 | SC Paderborn 07 | - | KFC Uerdingen 05 | 1:1 | ||||
| 7. Round | 13/09/2003 | Eintracht Braunschweig | - | SC Paderborn 07 | 2:0 | ||||
| 8. Round | 20/09/2003 | SC Paderborn 07 | - | SG Wattenscheid 09 | 3:2 | ||||
| 9. Round | 27/09/2003 | FC St. Pauli | - | SC Paderborn 07 | 2:0 | ||||
| 10. Round | 04/10/2003 | SC Paderborn 07 | - | Dynamo Dresden | 1:1 | ||||
| 11. Round | 11/10/2003 | Wuppertaler SV | - | SC Paderborn 07 | 0:3 | ||||
| 12. Round | 18/10/2003 | SC Paderborn 07 | - | Hamburger SV II | 0:0 | ||||
| 13. Round | 24/10/2003 | Holstein Kiel | - | SC Paderborn 07 | 1:1 | ||||
| 14. Round | 02/11/2003 | SC Paderborn 07 | - | Rot-Weiss Essen | 2:1 | ||||
| 15. Round | 08/11/2003 | Chemnitzer FC | - | SC Paderborn 07 | 1:2 | ||||
| 16. Round | 15/11/2003 | Preußen Münster | - | SC Paderborn 07 | 3:1 |
Germany