| 1. Round | 05/03/2016 | JK Nõmme Kalju | - | JK Sillamäe Kalev | 2:0 | ||||
| 2. Round | 09/03/2016 | FC Infonet | - | JK Nõmme Kalju | 2:1 | ||||
| 3. Round | 12/03/2016 | JK Nõmme Kalju | - | Rakvere JK Tarvas | 3:1 | ||||
| 4. Round | 19/03/2016 | JK Nõmme Kalju | - | FC Flora | 2:0 | ||||
| 5. Round | 02/04/2016 | FC Levadia | - | JK Nõmme Kalju | 1:1 | ||||
| 8. Round | 15/04/2016 | JK Tammeka | - | JK Nõmme Kalju | 0:3 | ||||
| 9. Round | 23/04/2016 | JK Nõmme Kalju | - | Paide Linnameeskond | 1:0 |  |
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| 17. Round | 26/04/2016 | JK Nõmme Kalju | - | FC Infonet | 2:1 | ||||
| 10. Round | 30/04/2016 | Paide Linnameeskond | - | JK Nõmme Kalju | 1:1 | ||||
| 11. Round | 07/05/2016 | JK Nõmme Kalju | - | JK Tammeka | 2:0 | ||||
| 15. Round | 10/05/2016 | FC Flora | - | JK Nõmme Kalju | 0:0 | ||||
| 12. Round | 14/05/2016 | JK Narva Trans | - | JK Nõmme Kalju | 1:1 | ||||
| 13. Round | 17/05/2016 | JK Nõmme Kalju | - | Pärnu Linnameeskond | 3:0 | ||||
| 14. Round | 24/05/2016 | JK Nõmme Kalju | - | FC Levadia | 0:1 | ||||
| 16. Round | 19/06/2016 | JK Sillamäe Kalev | - | JK Nõmme Kalju | 1:3 | ||||
| 18. Round | 10/07/2016 | Rakvere JK Tarvas | - | JK Nõmme Kalju | 1:6 |
Estonia