| 2. Round | 09/08/2006 | SV Wilhelmshaven | - | Hertha BSC II | 0:1 | ||||
| 3. Round | 13/08/2006 | 1. FC Union Berlin | - | SV Wilhelmshaven | 2:0 | ||||
| 5. Round | 25/08/2006 | SV Wilhelmshaven | - | Bayer Leverkusen II | 2:1 |  |
|||
| 6. Round | 02/09/2006 | Kickers Emden | - | SV Wilhelmshaven | 1:3 | ||||
| 7. Round | 12/09/2006 | SV Wilhelmshaven | - | FC St. Pauli | 3:3 | ||||
| 8. Round | 16/09/2006 | Hamburger SV II | - | SV Wilhelmshaven | 3:1 | ||||
| 11. Round | 14/10/2006 | SV Wilhelmshaven | - | Rot Weiss Ahlen | 4:1 | |
|||
| 12. Round | 20/10/2006 | VfL Osnabrück | - | SV Wilhelmshaven | 2:0 | ||||
| 13. Round | 28/10/2006 | SV Wilhelmshaven | - | Fortuna Düsseldorf | 1:1 | |
 |
||
| 14. Round | 04/11/2006 | Rot-Weiß Erfurt | - | SV Wilhelmshaven | 1:0 | ||||
| 15. Round | 08/11/2006 | SV Wilhelmshaven | - | Dynamo Dresden | 1:1 | |
|||
| 16. Round | 11/11/2006 | 1. FC Magdeburg | - | SV Wilhelmshaven | 3:0 | ||||
| 17. Round | 18/11/2006 | SV Wilhelmshaven | - | Wuppertaler SV | 2:1 | |
 |
||
| 19. Round | 02/12/2006 | SV Wilhelmshaven | - | VfB Lübeck | 1:3 | |
Poland