| 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 | ||||
| 4. Round | 17/08/2008 | NK Inter Zaprešić | - | NK Croatia Sesvete | 3:2 | |
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| 5. Round | 24/08/2008 | HNK Cibalia | - | NK Inter Zaprešić | 4:3 | ||||
| 6. Round | 31/08/2008 | NK Inter Zaprešić | - | NK Zadar | 3:1 | |
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| 7. Round | 14/09/2008 | NK Varteks | - | NK Inter Zaprešić | 1:0 | ||||
| 10. Round | 05/10/2008 | NK Inter Zaprešić | - | Slaven Belupo | 0:0 | ||||
| 11. Round | 19/10/2008 | NK Osijek | - | NK Inter Zaprešić | 2:1 | ||||
| 12. Round | 26/10/2008 | HNK Šibenik | - | NK Inter Zaprešić | 1:1 | ||||
| 13. Round | 02/11/2008 | NK Inter Zaprešić | - | Dinamo Zagreb | 1:3 | ||||
| 16. Round | 23/11/2008 | NK Inter Zaprešić | - | HNK Cibalia | 1:2 | ||||
| 20. Round | 01/03/2009 | NK Inter Zaprešić | - | Hajduk Split | 0:4 | ||||
| 21. Round | 08/03/2009 | Slaven Belupo | - | NK Inter Zaprešić | 1:0 | ||||
| 22. Round | 15/03/2009 | NK Inter Zaprešić | - | NK Osijek | 0:1 | ||||
| 24. Round | 05/04/2009 | NK Inter Zaprešić | - | Slaven Belupo | 1:0 |  |
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| 28. Round | 26/04/2009 | NK Inter Zaprešić | - | HNK Cibalia | 0:0 |
Bosnia-Herzegovina
Croatia