| 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 | ||||
| 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 | ||||
| 30. Round | 26/04/2017 | Lokomotiva Zagreb | - | NK Istra 1961 | 1:0 | ||||
| 31. Round | 30/04/2017 | NK Istra 1961 | - | Hajduk Split | 0:2 | ||||
| 32. Round | 07/05/2017 | Slaven Belupo | - | NK Istra 1961 | 2:0 | ||||
| 33. Round | 12/05/2017 | NK Istra 1961 | - | HNK Cibalia | 1:2 |
Croatia