| 3. Round | 11/08/1999 | Eintracht Trier | - | SC Paderborn 07 | 4:1 | ||||
| 4. Round | 15/08/1999 | SC Paderborn 07 | - | FK Pirmasens | 1:1 |  |
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| 5. Round | 22/08/1999 | SC Paderborn 07 | - | SV 07 Elversberg | 2:2 | ||||
| 6. Round | 29/08/1999 | Borussia Dortmund II | - | SC Paderborn 07 | 3:0 | ||||
| 11. Round | 03/10/1999 | SC Paderborn 07 | - | SC Verl | 0:0 | ||||
| 12. Round | 10/10/1999 | Preußen Münster | - | SC Paderborn 07 | 2:1 | ||||
| 13. Round | 17/10/1999 | SC Paderborn 07 | - | Bayer Leverkusen II | 2:2 | ||||
| 14. Round | 24/10/1999 | SC 07 Idar-Oberstein | - | SC Paderborn 07 | 0:3 | ||||
| 15. Round | 30/10/1999 | SC Paderborn 07 | - | Rot-Weiss Essen | 2:1 | ||||
| 26. Round | 05/03/2000 | VfL Bochum II | - | SC Paderborn 07 | 1:4 | ||||
| 32. Round | 15/04/2000 | Bayer Leverkusen II | - | SC Paderborn 07 | 0:3 |
Germany