| 1. Round | 31/07/1998 | Waldhof Mannheim | - | Wacker Burghausen | 1:1 | ||||
| 2. Round | 07/08/1998 | Wacker Burghausen | - | SC Pfullendorf | 2:1 | ||||
| 23. Round | 20/03/1999 | Karlsruher SC II | - | Wacker Burghausen | 3:1 | ||||
| 24. Round | 27/03/1999 | Wacker Burghausen | - | FSV Frankfurt | 2:0 | ||||
| 25. Round | 01/04/1999 | SC Weismain | - | Wacker Burghausen | 1:1 | ||||
| 26. Round | 10/04/1999 | Wacker Burghausen | - | VfR Mannheim | 1:1 | ||||
| 27. Round | 17/04/1999 | SC Neukirchen | - | Wacker Burghausen | 2:2 |  |
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| 28. Round | 23/04/1999 | Wacker Burghausen | - | TSF Ditzingen | 3:0 | ||||
| 29. Round | 30/04/1999 | Kickers Offenbach | - | Wacker Burghausen | 2:2 | |
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| 30. Round | 07/05/1999 | Wacker Burghausen | - | Bayern München II | 0:0 | ||||
| 31. Round | 12/05/1999 | SSV Reutlingen | - | Wacker Burghausen | 1:2 |  |
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| 32. Round | 15/05/1999 | SV Wehen-Taunusstein | - | Wacker Burghausen | 3:2 | |
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| 33. Round | 21/05/1999 | Wacker Burghausen | - | FC Augsburg | 1:0 | ||||
| 34. Round | 28/05/1999 | 1. FC Schweinfurt 05 | - | Wacker Burghausen | 2:3 |
Germany