| 20. Round | 24/07/2016 | FC Levadia | - | Paide Linnameeskond | 7:1 |  |
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| 21. Round | 29/07/2016 | Pärnu Linnameeskond | - | FC Levadia | 0:4 | ||||
| 19. Round | 01/08/2016 | FC Flora | - | FC Levadia | 6:1 | ||||
| 22. Round | 06/08/2016 | FC Levadia | - | JK Sillamäe Kalev | 2:1 | ||||
| 23. Round | 13/08/2016 | FC Infonet | - | FC Levadia | 0:0 | ||||
| 24. Round | 16/08/2016 | JK Tammeka | - | FC Levadia | 1:2 |  |
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| 25. Round | 20/08/2016 | FC Levadia | - | Rakvere JK Tarvas | 4:0 | |
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| 26. Round | 23/08/2016 | FC Levadia | - | JK Nõmme Kalju | 1:2 | |
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| 27. Round | 26/08/2016 | JK Narva Trans | - | FC Levadia | 3:1 | |
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| 28. Round | 10/09/2016 | FC Levadia | - | JK Narva Trans | 5:0 | |
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| 30. Round | 17/09/2016 | Paide Linnameeskond | - | FC Levadia | 0:4 | |
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| 31. Round | 24/09/2016 | FC Levadia | - | JK Tammeka | 4:0 | ||||
| 32. Round | 01/10/2016 | FC Levadia | - | FC Infonet | 2:2 | |
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| 33. Round | 15/10/2016 | JK Sillamäe Kalev | - | FC Levadia | 3:2 | |
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| 35. Round | 29/10/2016 | Rakvere JK Tarvas | - | FC Levadia | 0:1 | |
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| 36. Round | 05/11/2016 | FC Levadia | - | FC Flora | 2:1 | |
Estonia