| 1. Jornada | 07.08.2016 | FK Pobeda Junior | - | FK Pelister | 0:2 | ||||
| 2. Jornada | 14.08.2016 | FK Pelister | - | FK Bregalnica Štip | 3:0 |  |
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| 3. Jornada | 21.08.2016 | Makedonija GP | - | FK Pelister | 2:2 | ||||
| 4. Jornada | 27.08.2016 | FK Pelister | - | FK Rabotnički | 3:0 | |
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| 5. Jornada | 11.09.2016 | FK Renova | - | FK Pelister | 2:0 | ||||
| 6. Jornada | 17.09.2016 | KF Shkupi | - | FK Pelister | 2:1 | |
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| 7. Jornada | 25.09.2016 | FK Pelister | - | Sileks Kratovo | 0:0 | ||||
| 8. Jornada | 28.09.2016 | Vardar Skopje | - | FK Pelister | 1:1 | ||||
| 9. Jornada | 02.10.2016 | FK Pelister | - | KF Shkëndija 79 | 1:2 | ||||
| 10. Jornada | 16.10.2016 | FK Pelister | - | FK Pobeda Junior | 2:0 | |
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| 11. Jornada | 23.10.2016 | FK Bregalnica Štip | - | FK Pelister | 0:0 | ||||
| 27. Jornada | 15.04.2017 | FK Pelister | - | KF Shkëndija 79 | 0:1 | ||||
| 30. Jornada | 30.04.2017 | FK Pelister | - | Makedonija GP | 3:1 | ||||
| 33. Jornada | 13.05.2017 | FK Pelister | - | KF Shkupi | 1:0 | ||||
| 34. Jornada | 21.05.2017 | Sileks Kratovo | - | FK Pelister | 3:3 | ||||
| 35. Jornada | 28.05.2017 | FK Pelister | - | Vardar Skopje | 2:3 |
Macedonia del Norte