| 3. Round | 10/08/2008 | Servette FC | - | FC Schaffhausen | 1:2 | ||||
| 5. Round | 23/08/2008 | FC Thun | - | FC Schaffhausen | 0:3 | ||||
| 6. Round | 30/08/2008 | FC Schaffhausen | - | FC Wil 1900 | 1:3 |  |
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| 7. Round | 13/09/2008 | FC Lausanne-Sport | - | FC Schaffhausen | 3:3 | ||||
| 8. Round | 29/09/2008 | FC Schaffhausen | - | FC St. Gallen | 0:1 | ||||
| 9. Round | 04/10/2008 | Yverdon Sport FC | - | FC Schaffhausen | 3:0 | ||||
| 12. Round | 09/11/2008 | FC Schaffhausen | - | FC Winterthur | 3:0 | ||||
| 13. Round | 16/11/2008 | FC Schaffhausen | - | FC Wohlen | 2:2 | ||||
| 14. Round | 29/11/2008 | FC Stade Nyonnais | - | FC Schaffhausen | 3:1 | ||||
| 15. Round | 08/12/2008 | FC Schaffhausen | - | FC Concordia Basel | 2:4 | |
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| 19. Round | 15/03/2009 | FC Schaffhausen | - | FC Thun | 2:2 | ||||
| 21. Round | 06/04/2009 | FC Schaffhausen | - | FC Lausanne-Sport | 0:0 | ||||
| 27. Round | 09/05/2009 | FC Wohlen | - | FC Schaffhausen | 0:0 | ||||
| 29. Round | 24/05/2009 | FC Schaffhausen | - | FC Stade Nyonnais | 3:0 | ||||
| 30. Round | 28/05/2009 | FC Concordia Basel | - | FC Schaffhausen | 3:0 |
Switzerland