| 1. Round | 10/08/2016 | Makedonija GP | - | FK Rabotnički | 0:4 | ||||
| 3. Round | 21/08/2016 | FK Rabotnički | - | FK Renova | 1:0 | ||||
| 4. Round | 27/08/2016 | FK Pelister | - | FK Rabotnički | 3:0 | ||||
| 7. Round | 24/09/2016 | FK Rabotnički | - | KF Shkëndija 79 | 1:3 | ||||
| 9. Round | 01/10/2016 | FK Rabotnički | - | FK Bregalnica Štip | 1:1 | ||||
| 12. Round | 30/10/2016 | FK Renova | - | FK Rabotnički | 1:1 |
Croatia