| 1. Round | 02/08/1998 | 1. FC Kaiserslautern II | - | SC Paderborn 07 | 2:1 | ||||
| 5. Round | 30/08/1998 | SC Paderborn 07 | - | Alemannia Aachen | 2:0 |  |
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| 9. Round | 27/09/1998 | SC Paderborn 07 | - | SC Verl | 2:2 |  |
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| 10. Round | 04/10/1998 | SV 07 Elversberg | - | SC Paderborn 07 | 3:0 | ||||
| 11. Round | 10/10/1998 | SC Paderborn 07 | - | Preußen Münster | 1:3 | ||||
| 15. Round | 08/11/1998 | SC Paderborn 07 | - | Eintracht Trier | 2:1 | ||||
| 14. Round | 21/11/1998 | LR Ahlen | - | SC Paderborn 07 | 3:1 | ||||
| 33. Round | 24/05/1999 | SC Paderborn 07 | - | Borussia Dortmund II | 2:1 | ||||
| 34. Round | 30/05/1999 | 1. FC Saarbrücken | - | SC Paderborn 07 | 1:1 |
Spain