| 12. Round | 20/11/2016 | Pembroke Athleta FC | - | Floriana FC | 1:2 | ||||
| 13. Round | 27/11/2016 | Balzan FC | - | Pembroke Athleta FC | 4:0 | ||||
| 14. Round | 03/12/2016 | Pembroke Athleta FC | - | Valletta FC | 0:3 | ||||
| 17. Round | 08/01/2017 | Birkirkara FC | - | Pembroke Athleta FC | 2:0 | ||||
| 19. Round | 22/01/2017 | Tarxien Rainbows | - | Pembroke Athleta FC | 7:1 | ||||
| 21. Round | 04/02/2017 | Sliema Wanderers | - | Pembroke Athleta FC | 1:1 | ||||
| 22. Round | 11/02/2017 | Pembroke Athleta FC | - | Mosta FC | 0:3 dec. | ||||
| 23. Round | 25/02/2017 | Floriana FC | - | Pembroke Athleta FC | 2:0 | ||||
| 24. Round | 05/03/2017 | Pembroke Athleta FC | - | Balzan FC | 2:5 | ||||
| 25. Round | 11/03/2017 | Valletta FC | - | Pembroke Athleta FC | 4:0 |  |
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| 26. Round | 17/03/2017 | Pembroke Athleta FC | - | Hibernians FC | 0:3 | ||||
| 27. Round | 01/04/2017 | Gżira United | - | Pembroke Athleta FC | 5:1 | |
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| 28. Round | 04/04/2017 | Pembroke Athleta FC | - | Birkirkara FC | 0:2 | |
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| 29. Round | 09/04/2017 | St. Andrews FC | - | Pembroke Athleta FC | 6:0 | ||||
| 33. Round | 05/05/2017 | Mosta FC | - | Pembroke Athleta FC | 4:2 |
Nigeria