| 1. Round | 16/07/2016 | NK Istra 1961 | - | NK Osijek | 0:1 | ||||
| 2. Round | 22/07/2016 | HNK Rijeka | - | NK Istra 1961 | 4:1 | ||||
| 3. Round | 31/07/2016 | NK Istra 1961 | - | Lokomotiva Zagreb | 1:1 | ||||
| 4. Round | 07/08/2016 | Hajduk Split | - | NK Istra 1961 | 4:0 | ||||
| 5. Round | 14/08/2016 | NK Istra 1961 | - | Slaven Belupo | 0:0 | ||||
| 6. Round | 20/08/2016 | HNK Cibalia | - | NK Istra 1961 | 1:1 | ||||
| 7. Round | 28/08/2016 | NK Istra 1961 | - | Dinamo Zagreb | 1:2 | ||||
| 8. Round | 10/09/2016 | RNK Split | - | NK Istra 1961 | 0:3 | ||||
| 9. Round | 17/09/2016 | NK Istra 1961 | - | NK Inter Zaprešić | 4:1 | ||||
| 12. Round | 15/10/2016 | Lokomotiva Zagreb | - | NK Istra 1961 | 2:1 | ||||
| 13. Round | 22/10/2016 | NK Istra 1961 | - | Hajduk Split | 0:0 |  |
|||
| 14. Round | 29/10/2016 | Slaven Belupo | - | NK Istra 1961 | 2:0 | |
|||
| 15. Round | 06/11/2016 | NK Istra 1961 | - | HNK Cibalia | 3:2 | ||||
| 16. Round | 18/11/2016 | Dinamo Zagreb | - | NK Istra 1961 | 1:1 | ||||
| 17. Round | 26/11/2016 | NK Istra 1961 | - | RNK Split | 1:0 | ||||
| 18. Round | 05/12/2016 | NK Inter Zaprešić | - | NK Istra 1961 | 2:2 | ||||
| 19. Round | 10/12/2016 | NK Istra 1961 | - | NK Osijek | 1:3 | ||||
| 20. Round | 17/12/2016 | HNK Rijeka | - | NK Istra 1961 | 1:0 |
Bulgaria