| 3. Round | 23/08/2008 | FC Pirin | - | PFC Litex Lovech | 1:1 | ||||
| 4. Round | 30/08/2008 | Lokomotiv 2012 Mezdra | - | FC Pirin | 4:0 | ||||
| 5. Round | 15/09/2008 | FC Pirin | - | Belasitsa Petrich | 2:0 |  |
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| 6. Round | 20/09/2008 | OFC Sliven | - | FC Pirin | 2:1 | ||||
| 7. Round | 27/09/2008 | FC Pirin | - | CSKA Sofia | 2:2 |  |
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| 8. Round | 04/10/2008 | Spartak Varna | - | FC Pirin | 2:0 | ||||
| 9. Round | 21/10/2008 | FC Pirin | - | Slavia Sofia | 3:2 | |
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| 10. Round | 25/10/2008 | Minyor Pernik | - | FC Pirin | 0:0 | ||||
| 11. Round | 01/11/2008 | FC Pirin | - | Lokomotiv Plovdiv | 1:0 | ||||
| 12. Round | 07/11/2008 | FC Pirin | - | Vihren Sandanski | 2:1 | |
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| 13. Round | 15/11/2008 | Botev Plovdiv | - | FC Pirin | 1:0 | ||||
| 14. Round | 23/11/2008 | FC Pirin | - | PSFC Chernomorets | 2:1 | ||||
| 15. Round | 29/11/2008 | Levski Sofia | - | FC Pirin | 2:0 | ||||
| 16. Round | 08/03/2009 | Cherno More Varna | - | Pirin Blagoevgrad | 1:0 | ||||
| 17. Round | 13/03/2009 | Pirin Blagoevgrad | - | Lokomotiv Sofia | 0:4 |
Bulgaria