| 1. Round | 19/08/2016 | Birkirkara FC | - | St. Andrews FC | 4:0 | ||||
| 2. Round | 26/08/2016 | Tarxien Rainbows | - | Birkirkara FC | 0:4 | ||||
| 3. Round | 11/09/2016 | Birkirkara FC | - | Hamrun Spartans | 2:1 |  |
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| 4. Round | 18/09/2016 | Sliema Wanderers | - | Birkirkara FC | 2:1 | ||||
| 5. Round | 22/09/2016 | Birkirkara FC | - | Mosta FC | 2:0 | |
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| 7. Round | 30/09/2016 | Valletta FC | - | Birkirkara FC | 1:1 |  |
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| 10. Round | 30/10/2016 | Birkirkara FC | - | Hibernians FC | 0:1 | ||||
| 15. Round | 11/12/2016 | Birkirkara FC | - | Sliema Wanderers | 1:2 | ||||
| 16. Round | 04/01/2017 | Mosta FC | - | Birkirkara FC | 0:2 |  |
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| 17. Round | 08/01/2017 | Birkirkara FC | - | Pembroke Athleta FC | 2:0 | ||||
| 18. Round | 15/01/2017 | Balzan FC | - | Birkirkara FC | 1:1 | ||||
| 20. Round | 29/01/2017 | Hibernians FC | - | Birkirkara FC | 1:2 | ||||
| 22. Round | 11/02/2017 | Birkirkara FC | - | Floriana FC | 1:2 | ||||
| 23. Round | 25/02/2017 | Birkirkara FC | - | St. Andrews FC | 2:2 | |
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| 24. Round | 04/03/2017 | Tarxien Rainbows | - | Birkirkara FC | 0:1 | |
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| 28. Round | 04/04/2017 | Pembroke Athleta FC | - | Birkirkara FC | 0:2 | |
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| 31. Round | 23/04/2017 | Birkirkara FC | - | Hibernians FC | 2:0 | ||||
| 32. Round | 30/04/2017 | Gżira United | - | Birkirkara FC | 1:1 | |
Serbia