| 14. Round | 15/02/2009 | Werder Bremen [Youth] | - | Rot-Weiß Erfurt [Youth] | 4:0 | ||||
| 15. Round | 21/02/2009 | FC St. Pauli [Youth] | - | Werder Bremen [Youth] | 3:4 | ||||
| 17. Round | 08/03/2009 | Werder Bremen [Youth] | - | Hannover 96 [Youth] | 3:1 | ||||
| 12. Round | 11/03/2009 | Hamburger SV [Youth] | - | Werder Bremen [Youth] | 0:3 | ||||
| 18. Round | 15/03/2009 | Energie Cottbus [Youth] | - | Werder Bremen [Youth] | 1:2 | ||||
| 19. Round | 22/03/2009 | Werder Bremen [Youth] | - | VfL Osnabrück [Youth] | 3:1 |  |
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| 20. Round | 05/04/2009 | VfL Wolfsburg [Youth] | - | Werder Bremen [Youth] | 1:0 | ||||
| 21. Round | 19/04/2009 | Werder Bremen [Youth] | - | Eintracht Braunschweig [Youth] | 6:3 | |
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| 22. Round | 25/04/2009 | 1. FC Union Berlin [Youth] | - | Werder Bremen [Youth] | 2:2 | |
Hungary