| 22/07/2016 | 17:00 | JK Tammeka | - | FC Flora | 0:4 (0:2) | |
| 23/07/2016 | 14:00 | JK Narva Trans | - | JK Sillamäe Kalev | 1:3 (1:1) | |
| 17:00 | FC Infonet | - | Rakvere JK Tarvas | 6:0 (2:0) | ||
| 24/07/2016 | 17:00 | JK Nõmme Kalju | - | Pärnu Linnameeskond | 0:0 (0:0) | |
| 17:00 | FC Levadia | - | Paide Linnameeskond | 7:1 (3:1) |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
FC Infonet | 20 | 14 | 4 | 2 | 48:19 | 29 | 46 |
| 2 |
|
FC Levadia | 20 | 13 | 4 | 3 | 38:17 | 21 | 43 |
| 3 |
|
JK Nõmme Kalju | 20 | 12 | 6 | 2 | 40:12 | 28 | 42 |
| 4 |
|
FC Flora | 20 | 10 | 7 | 3 | 47:14 | 33 | 37 |
| 5 |
|
JK Sillamäe Kalev | 20 | 7 | 7 | 6 | 30:25 | 5 | 28 |
| 6 |
|
JK Tammeka | 20 | 7 | 5 | 8 | 21:31 | -10 | 26 |
| 7 |
|
Paide Linnameeskond | 20 | 7 | 4 | 9 | 31:35 | -4 | 25 |
| 8 |
|
JK Narva Trans | 20 | 5 | 5 | 10 | 29:40 | -11 | 20 |
| 9 |
|
Pärnu Linnameeskond | 20 | 3 | 1 | 16 | 9:43 | -34 | 10 |
| 10 |
|
Rakvere JK Tarvas | 20 | 0 | 1 | 19 | 9:66 | -57 | 1 |
| Champions League Quali. | |
| Playoffs | |
| Relegation |