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| 1st(1st leg) | Metalurg Skopje | - | Mladost Carev Dvor | dnp | ||
| 2nd (2nd leg) | Mladost Carev Dvor | - | Metalurg Skopje | dnp | ||
| 1st(1st leg): 21/09/2016 | 2nd (2nd leg): 12/10/2016 | Winner: Metalurg Skopje | ||||
| 1st(1st leg) | Akademija Pandev | - | KF Shkupi | 0:1 (0:0) | ||
| 2nd (2nd leg) | KF Shkupi | - | Akademija Pandev | 3:1 | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 12/10/2016 13:30 | Winner: KF Shkupi | ||||
| 1st(1st leg) | FK Pelister | - | FK Renova | 2:0 (2:0) | ||
| 2nd (2nd leg) | FK Renova | - | FK Pelister | 3:1 (3:0) | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 19/10/2016 13:30 | Winner: FK Pelister | ||||
| 1st(1st leg) | FK Vlazrimi 77 | - | Vardar Skopje | 1:3 (1:0) | ||
| 2nd (2nd leg) | Vardar Skopje | - | FK Vlazrimi 77 | 2:0 (1:0) | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 19/10/2016 13:30 | Winner: Vardar Skopje | ||||
| 1st(1st leg) | Sileks Kratovo | - | FK Turnovo | 2:1 (1:0) | ||
| 2nd (2nd leg) | FK Turnovo | - | Sileks Kratovo | 3:3 (2:2) | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 12/10/2016 13:30 | Winner: Sileks Kratovo | ||||
| 1st(1st leg) | FK Bregalnica Štip | - | FK Teteks | 4:0 (2:0) | ||
| 2nd (2nd leg) | FK Teteks | - | FK Bregalnica Štip | 1:2 (0:0) | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 12/10/2016 13:30 | Winner: FK Bregalnica Štip | ||||
| 1st(1st leg) | FK Novaci 2005 | - | FK Pobeda Junior | 1:2 (0:0) | ||
| 2nd (2nd leg) | FK Pobeda Junior | - | FK Novaci 2005 | 5:0 | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 12/10/2016 13:30 | Winner: FK Pobeda Junior | ||||
| 1st(1st leg) | FK Rabotnički | - | KF Shkëndija 79 | 0:2 (0:0) | ||
| 2nd (2nd leg) | KF Shkëndija 79 | - | FK Rabotnički | 0:0 (0:0) | ||
| 1st(1st leg): 21/09/2016 14:30 | 2nd (2nd leg): 19/10/2016 13:30 | Winner: KF Shkëndija 79 | ||||
