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| I | Metalurg Skopje | - | Mladost Carev Dvor | no jug. | ||
| V | Mladost Carev Dvor | - | Metalurg Skopje | no jug. | ||
| I: 21.09.2016 | V: 12.10.2016 | Campeones: Metalurg Skopje | ||||
| I | FK AP Brera Strumica | - | KF Shkupi | 0:1 (0:0) | ||
| V | KF Shkupi | - | FK AP Brera Strumica | 3:1 | ||
| I: 21.09.2016 15:30 | V: 12.10.2016 14:30 | Campeones: KF Shkupi | ||||
| I | FK Pelister | - | FK Renova | 2:0 (2:0) | ||
| V | FK Renova | - | FK Pelister | 3:1 (3:0) | ||
| I: 21.09.2016 15:30 | V: 19.10.2016 14:30 | Campeones: FK Pelister | ||||
| I | FK Vlazrimi 77 | - | Vardar Skopje | 1:3 (1:0) | ||
| V | Vardar Skopje | - | FK Vlazrimi 77 | 2:0 (1:0) | ||
| I: 21.09.2016 15:30 | V: 19.10.2016 14:30 | Campeones: Vardar Skopje | ||||
| I | Sileks Kratovo | - | FK Turnovo | 2:1 (1:0) | ||
| V | FK Turnovo | - | Sileks Kratovo | 3:3 (2:2) | ||
| I: 21.09.2016 15:30 | V: 12.10.2016 14:30 | Campeones: Sileks Kratovo | ||||
| I | FK Bregalnica Štip | - | FK Teteks | 4:0 (2:0) | ||
| V | FK Teteks | - | FK Bregalnica Štip | 1:2 (0:0) | ||
| I: 21.09.2016 15:30 | V: 12.10.2016 14:30 | Campeones: FK Bregalnica Štip | ||||
| I | FK Novaci 2005 | - | FK Pobeda Junior | 1:2 (0:0) | ||
| V | FK Pobeda Junior | - | FK Novaci 2005 | 5:0 | ||
| I: 21.09.2016 15:30 | V: 12.10.2016 14:30 | Campeones: FK Pobeda Junior | ||||
| I | FK Rabotnički | - | KF Shkëndija 79 | 0:2 (0:0) | ||
| V | KF Shkëndija 79 | - | FK Rabotnički | 0:0 (0:0) | ||
| I: 21.09.2016 15:30 | V: 19.10.2016 14:30 | Campeones: KF Shkëndija 79 | ||||
