| 1. Round | 27/07/2008 | NK Inter Zaprešić | - | HNK Šibenik | 2:3 |  |
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| 2. Round | 03/08/2008 | Dinamo Zagreb | - | NK Inter Zaprešić | 3:1 | ||||
| 3. Round | 10/08/2008 | NK Inter Zaprešić | - | HNK Rijeka | 2:2 | |
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| 4. Round | 17/08/2008 | NK Inter Zaprešić | - | NK Croatia Sesvete | 3:2 | ||||
| 5. Round | 24/08/2008 | HNK Cibalia | - | NK Inter Zaprešić | 4:3 | |
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| 8. Round | 21/09/2008 | NK Inter Zaprešić | - | NK Zagreb | 1:1 | ||||
| 12. Round | 26/10/2008 | HNK Šibenik | - | NK Inter Zaprešić | 1:1 | |
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| 14. Round | 09/11/2008 | HNK Rijeka | - | NK Inter Zaprešić | 0:1 | ||||
| 15. Round | 16/11/2008 | NK Croatia Sesvete | - | NK Inter Zaprešić | 1:3 | ||||
| 16. Round | 23/11/2008 | NK Inter Zaprešić | - | HNK Cibalia | 1:2 | ||||
| 17. Round | 30/11/2008 | NK Zadar | - | NK Inter Zaprešić | 1:1 | ||||
| 18. Round | 07/12/2008 | NK Inter Zaprešić | - | NK Varteks | 2:3 | |
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| 19. Round | 22/02/2009 | NK Zagreb | - | NK Inter Zaprešić | 0:1 | ||||
| 20. Round | 01/03/2009 | NK Inter Zaprešić | - | Hajduk Split | 0:4 | |
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| 22. Round | 15/03/2009 | NK Inter Zaprešić | - | NK Osijek | 0:1 | ||||
| 23. Round | 22/03/2009 | HNK Šibenik | - | NK Inter Zaprešić | 4:0 |
Bosnia-Herzegovina