| 1. Round | 28/07/2000 | Wacker Burghausen | - | VfR Aalen | 1:1 | ||||
| 2. Round | 05/08/2000 | SV Wehen-Taunusstein | - | Wacker Burghausen | 2:1 | ||||
| 4. Round | 20/08/2000 | Sportfreunde Siegen | - | Wacker Burghausen | 3:2 | ||||
| 5. Round | 26/08/2000 | Wacker Burghausen | - | TSV 1860 München II | 4:2 | ||||
| 6. Round | 02/09/2000 | Karlsruher SC | - | Wacker Burghausen | 3:0 | ||||
| 8. Round | 19/09/2000 | SV Darmstadt 98 | - | Wacker Burghausen | 5:1 |  |
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| 9. Round | 22/09/2000 | SC Pfullendorf | - | Wacker Burghausen | 2:0 | ||||
| 10. Round | 30/09/2000 | Wacker Burghausen | - | Jahn Regensburg | 2:1 | |
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| 11. Round | 06/10/2000 | Eintracht Trier | - | Wacker Burghausen | 3:0 | |
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| 13. Round | 22/10/2000 | Bayern München II | - | Wacker Burghausen | 3:1 |
Germany