| 4. Round | 18/03/2016 | JK Narva Trans | - | FC Levadia | 1:1 | ||||
| 8. Round | 16/04/2016 | JK Narva Trans | - | Pärnu Linnameeskond | 4:0 | ||||
| 15. Round | 10/05/2016 | FC Levadia | - | JK Narva Trans | 1:0 | ||||
| 14. Round | 24/05/2016 | JK Narva Trans | - | FC Flora | 1:2 | ||||
| 20. Round | 23/07/2016 | JK Narva Trans | - | JK Sillamäe Kalev | 1:3 |  |
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| 21. Round | 30/07/2016 | FC Infonet | - | JK Narva Trans | 4:3 | ||||
| 22. Round | 06/08/2016 | FC Flora | - | JK Narva Trans | 4:1 | ||||
| 24. Round | 15/08/2016 | JK Nõmme Kalju | - | JK Narva Trans | 2:0 | ||||
| 25. Round | 19/08/2016 | JK Narva Trans | - | Pärnu Linnameeskond | 3:1 | ||||
| 26. Round | 23/08/2016 | JK Tammeka | - | JK Narva Trans | 0:2 | ||||
| 27. Round | 26/08/2016 | JK Narva Trans | - | FC Levadia | 3:1 | ||||
| 28. Round | 10/09/2016 | FC Levadia | - | JK Narva Trans | 5:0 | ||||
| 29. Round | 13/09/2016 | JK Narva Trans | - | JK Tammeka | 4:2 | ||||
| 31. Round | 24/09/2016 | JK Narva Trans | - | JK Nõmme Kalju | 0:3 | ||||
| 32. Round | 01/10/2016 | Rakvere JK Tarvas | - | JK Narva Trans | 0:6 | ||||
| 33. Round | 15/10/2016 | JK Narva Trans | - | FC Flora | 0:2 |
Estonia