| 3. Round | 12/03/2016 | FC Flora | - | JK Narva Trans | 3:0 | ||||
| 4. Round | 18/03/2016 | JK Narva Trans | - | FC Levadia | 1:1 | ||||
| 5. Round | 02/04/2016 | JK Narva Trans | - | Rakvere JK Tarvas | 2:2 | ||||
| 6. Round | 05/04/2016 | JK Narva Trans | - | Paide Linnameeskond | 2:3 | ||||
| 7. Round | 09/04/2016 | JK Nõmme Kalju | - | JK Narva Trans | 6:0 |  |
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| 8. Round | 16/04/2016 | JK Narva Trans | - | Pärnu Linnameeskond | 4:0 | |
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| 9. Round | 23/04/2016 | JK Narva Trans | - | FC Infonet | 0:3 | |
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| 10. Round | 29/04/2016 | Rakvere JK Tarvas | - | JK Narva Trans | 0:1 | ||||
| 11. Round | 06/05/2016 | Pärnu Linnameeskond | - | JK Narva Trans | 0:1 | ||||
| 15. Round | 10/05/2016 | FC Levadia | - | JK Narva Trans | 1:0 | |
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| 13. Round | 17/05/2016 | FC Infonet | - | JK Narva Trans | 2:1 | ||||
| 16. Round | 19/06/2016 | JK Narva Trans | - | JK Tammeka | 4:1 | ||||
| 17. Round | 02/07/2016 | Paide Linnameeskond | - | JK Narva Trans | 3:2 | ||||
| 18. Round | 08/07/2016 | JK Sillamäe Kalev | - | JK Narva Trans | 3:0 |
Estonia