| 2. Round | 30/07/2016 | FC Saxan | - | FC Academia UTM | 1:0 | ||||
| 3. Round | 06/08/2016 | FC Academia UTM | - | FC Zimbru | 0:2 |  |
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| 5. Round | 20/08/2016 | FC Academia UTM | - | FC Milsami | 0:4 | ||||
| 7. Round | 11/09/2016 | Speranţa Nisporeni | - | FC Academia UTM | 0:1 | ||||
| 8. Round | 17/09/2016 | FC Academia UTM | - | FC Sheriff | 0:1 | ||||
| 9. Round | 25/09/2016 | CS Petrocub | - | FC Academia UTM | 0:1 | ||||
| 10. Round | 30/09/2016 | FC Academia UTM | - | FC Zaria | 0:2 | ||||
| 11. Round | 15/10/2016 | Dinamo-Auto | - | FC Academia UTM | 3:1 |  |
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| 12. Round | 21/10/2016 | CF Ungheni | - | FC Academia UTM | 1:2 |  |
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| 13. Round | 29/10/2016 | FC Academia UTM | - | FC Saxan | 1:0 | ||||
| 14. Round | 05/11/2016 | FC Zimbru | - | FC Academia UTM | 2:0 | |
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| 16. Round | 25/11/2016 | FC Milsami | - | FC Academia UTM | 2:0 | ||||
| 18. Round | 04/12/2016 | FC Academia UTM | - | Speranţa Nisporeni | 3:1 | |
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| 19. Round | 10/12/2016 | FC Sheriff | - | FC Academia UTM | 1:0 |
Moldova