| 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 | ||||
| 7. Round | 05/09/1999 | SC Paderborn 07 | - | VfL Bochum II | 1:1 |  |
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| 8. Round | 12/09/1999 | Fortuna Düsseldorf | - | SC Paderborn 07 | 0:0 | ||||
| 9. Round | 19/09/1999 | SC Paderborn 07 | - | KFC Uerdingen 05 | 1:0 | ||||
| 10. Round | 26/09/1999 | FSV Salmrohr | - | SC Paderborn 07 | 1:2 | ||||
| 13. Round | 17/10/1999 | SC Paderborn 07 | - | Bayer Leverkusen II | 2:2 | ||||
| 17. Round | 14/11/1999 | SC Paderborn 07 | - | SG Wattenscheid 09 | 1:2 | ||||
| 18. Round | 28/11/1999 | Sportfreunde Siegen | - | SC Paderborn 07 | 1:0 | ||||
| 19. Round | 05/12/1999 | SC Paderborn 07 | - | 1. FC Kaiserslautern II | 0:1 |
Germany