| 22. Round | 07/08/2016 | JK Nõmme Kalju | - | Paide Linnameeskond | 1:1 |  |
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| 23. Round | 12/08/2016 | JK Sillamäe Kalev | - | JK Nõmme Kalju | 0:1 | ||||
| 24. Round | 15/08/2016 | JK Nõmme Kalju | - | JK Narva Trans | 2:0 | ||||
| 25. Round | 20/08/2016 | JK Nõmme Kalju | - | JK Tammeka | 3:0 | ||||
| 26. Round | 23/08/2016 | FC Levadia | - | JK Nõmme Kalju | 1:2 | ||||
| 27. Round | 27/08/2016 | JK Nõmme Kalju | - | FC Flora | 3:3 |  |
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| 28. Round | 10/09/2016 | FC Flora | - | JK Nõmme Kalju | 1:1 | ||||
| 29. Round | 13/09/2016 | JK Nõmme Kalju | - | FC Levadia | 0:3 | |
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| 30. Round | 17/09/2016 | Pärnu Linnameeskond | - | JK Nõmme Kalju | 1:5 | ||||
| 31. Round | 24/09/2016 | JK Narva Trans | - | JK Nõmme Kalju | 0:3 | ||||
| 19. Round | 27/09/2016 | FC Infonet | - | JK Nõmme Kalju | 2:2 | |
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| 32. Round | 01/10/2016 | JK Nõmme Kalju | - | JK Sillamäe Kalev | 3:1 | ||||
| 33. Round | 15/10/2016 | Paide Linnameeskond | - | JK Nõmme Kalju | 2:0 | ||||
| 34. Round | 22/10/2016 | JK Nõmme Kalju | - | Rakvere JK Tarvas | 2:0 | ||||
| 21. Round | 25/10/2016 | Rakvere JK Tarvas | - | JK Nõmme Kalju | 1:2 | |
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| 36. Round | 05/11/2016 | JK Nõmme Kalju | - | FC Infonet | 1:2 |
Estonia