| 1. Round | 27/07/2008 | Bayern München II | - | 1. FC Union Berlin | 2:1 | ||||
| 8. Round | 28/09/2008 | FC Carl Zeiss Jena | - | 1. FC Union Berlin | 1:2 | ||||
| 9. Round | 04/10/2008 | 1. FC Union Berlin | - | VfR Aalen | 3:0 | ||||
| 12. Round | 28/10/2008 | Stuttgarter Kickers | - | 1. FC Union Berlin | 2:2 | ||||
| 14. Round | 08/11/2008 | SpVgg Unterhaching | - | 1. FC Union Berlin | 1:0 | ||||
| 21. Round | 07/02/2009 | VfB Stuttgart II | - | 1. FC Union Berlin | 0:3 |
Germany