| 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 | ||||
| 10. Round | 30/04/2016 | Paide Linnameeskond | - | JK Nõmme Kalju | 1:1 | ||||
| 13. Round | 17/05/2016 | JK Nõmme Kalju | - | Pärnu Linnameeskond | 3:0 |  |
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| 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 | ||||
| 20. Round | 24/07/2016 | JK Nõmme Kalju | - | Pärnu Linnameeskond | 0:0 | ||||
| 32. Round | 01/10/2016 | JK Nõmme Kalju | - | JK Sillamäe Kalev | 3:1 |
Estonia