| 1. Round | 16/08/2008 | 1. FC Heidenheim 1846 | - | SC Pfullendorf | 1:2 | ||||
| 6. Round | 27/09/2008 | SC Pfullendorf | - | Karlsruher SC II | 3:2 | ||||
| 9. Round | 25/10/2008 | SC Pfullendorf | - | SSV Ulm 1846 | 2:1 | ||||
| 10. Round | 29/10/2008 | 1. FC Eintracht Bamberg | - | SC Pfullendorf | 1:1 | ||||
| 12. Round | 07/11/2008 | Hessen Kassel | - | SC Pfullendorf | 2:0 | ||||
| 14. Round | 22/11/2008 | SpVgg Greuther Fürth II | - | SC Pfullendorf | 5:1 |  |
Germany