| 4. Round | 22/08/1999 | VfB Stuttgart II | - | Wacker Burghausen | 1:0 | ||||
| 5. Round | 27/08/1999 | Wacker Burghausen | - | FSV Frankfurt | 1:0 | ||||
| 6. Round | 31/08/1999 | Quelle Fürth | - | Wacker Burghausen | 2:2 |  |
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| 8. Round | 11/09/1999 | SV Darmstadt 98 | - | Wacker Burghausen | 2:2 | ||||
| 9. Round | 19/09/1999 | VfR Mannheim | - | Wacker Burghausen | 2:1 | |
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| 10. Round | 24/09/1999 | Wacker Burghausen | - | Karlsruher SC II | 1:4 | ||||
| 13. Round | 16/10/1999 | Borussia Fulda | - | Wacker Burghausen | 0:1 |
Albania