| 1. Jornada | 27.07.2008 | NK Inter Zaprešić | - | HNK Šibenik | 2:3 | ||||
| 4. Jornada | 17.08.2008 | NK Inter Zaprešić | - | NK Croatia Sesvete | 3:2 | ||||
| 5. Jornada | 24.08.2008 | HNK Cibalia | - | NK Inter Zaprešić | 4:3 | ||||
| 6. Jornada | 31.08.2008 | NK Inter Zaprešić | - | NK Zadar | 3:1 | ||||
| 7. Jornada | 14.09.2008 | NK Varteks | - | NK Inter Zaprešić | 1:0 | ||||
| 8. Jornada | 21.09.2008 | NK Inter Zaprešić | - | NK Zagreb | 1:1 | ||||
| 9. Jornada | 28.09.2008 | Hajduk Split | - | NK Inter Zaprešić | 3:3 | ||||
| 10. Jornada | 05.10.2008 | NK Inter Zaprešić | - | Slaven Belupo | 0:0 | ||||
| 19. Jornada | 22.02.2009 | NK Zagreb | - | NK Inter Zaprešić | 0:1 | ||||
| 20. Jornada | 01.03.2009 | NK Inter Zaprešić | - | Hajduk Split | 0:4 | ||||
| 21. Jornada | 08.03.2009 | Slaven Belupo | - | NK Inter Zaprešić | 1:0 | ||||
| 22. Jornada | 15.03.2009 | NK Inter Zaprešić | - | NK Osijek | 0:1 | ||||
| 24. Jornada | 05.04.2009 | NK Inter Zaprešić | - | Slaven Belupo | 1:0 |  |
Croacia