| 1. Round | 02/08/2008 | Tescoma Zlín | - | FK Baumit Jablonec | 0:1 | ||||
| 2. Round | 11/08/2008 | FK Baumit Jablonec | - | Baník Ostrava | 2:1 | ||||
| 3. Round | 17/08/2008 | FK Baumit Jablonec | - | FK Mladá Boleslav | 1:1 |  |
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| 4. Round | 24/08/2008 | Sigma Olomouc | - | FK Baumit Jablonec | 1:1 | ||||
| 5. Round | 31/08/2008 | FK Baumit Jablonec | - | SK Kladno | 1:1 | ||||
| 6. Round | 15/09/2008 | Slavia Praha | - | FK Baumit Jablonec | 2:0 | ||||
| 7. Round | 21/09/2008 | FK Baumit Jablonec | - | Viktoria Žižkov | 2:0 | |
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| 8. Round | 28/09/2008 | Dynamo České Budějovice | - | FK Baumit Jablonec | 2:1 | ||||
| 9. Round | 05/10/2008 | FK Baumit Jablonec | - | 1. FC Brno | 2:0 | ||||
| 10. Round | 20/10/2008 | Slovan Liberec | - | FK Baumit Jablonec | 3:0 | ||||
| 11. Round | 26/10/2008 | FK Baumit Jablonec | - | FK Teplice | 0:2 |  |
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| 15. Round | 24/11/2008 | FK Baumit Jablonec | - | AC Sparta Praha | 1:0 | ||||
| 21. Round | 22/03/2009 | Viktoria Žižkov | - | FK Baumit Jablonec | 0:1 | ||||
| 24. Round | 18/04/2009 | FK Baumit Jablonec | - | Slovan Liberec | 0:1 | ||||
| 25. Round | 26/04/2009 | FK Teplice | - | FK Baumit Jablonec | 3:0 | |
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| 26. Round | 03/05/2009 | FK Baumit Jablonec | - | Viktoria Plzeň | 3:0 | |
Czech Republic