| 18. Round | 05/02/2000 | 1. FC Union Berlin | - | Rot-Weiß Erfurt | 3:0 | ||||
| 19. Round | 12/02/2000 | Hertha BSC II | - | 1. FC Union Berlin | 0:1 | ||||
| 20. Round | 20/02/2000 | 1. FC Union Berlin | - | VfL Halle 96 | 2:2 | ||||
| 22. Round | 04/03/2000 | 1. FC Union Berlin | - | Sachsen Leipzig | 1:1 | ||||
| 23. Round | 11/03/2000 | VFC Plauen | - | 1. FC Union Berlin | 0:1 |  |
|||
| 24. Round | 19/03/2000 | 1. FC Union Berlin | - | Lok Altmark Stendal | 2:0 | ||||
| 25. Round | 25/03/2000 | Erzgebirge Aue | - | 1. FC Union Berlin | 2:1 | ||||
| 27. Round | 11/04/2000 | SV Babelsberg 03 | - | 1. FC Union Berlin | 0:1 | ||||
| 28. Round | 15/04/2000 | Stahl Eisenhüttenstadt | - | 1. FC Union Berlin | 0:1 | ||||
| 29. Round | 22/04/2000 | 1. FC Union Berlin | - | BFC Dynamo | 2:1 | ||||
| 26. Round | 25/04/2000 | 1. FC Union Berlin | - | FC Carl Zeiss Jena | 2:0 |  |
|||
| 30. Round | 29/04/2000 | Dresdner SC | - | 1. FC Union Berlin | 1:2 | ||||
| 31. Round | 05/05/2000 | 1. FC Union Berlin | - | VfB Leipzig | 0:0 | ||||
| 32. Round | 10/05/2000 | TeBe Berlin II | - | 1. FC Union Berlin | 0:2 | ||||
| 33. Round | 13/05/2000 | 1. FC Union Berlin | - | 1. FC Magdeburg | 3:2 |
Lithuania