Second league 2016
| Rank | Teams | Played | Won | Drawn | Lost | GD | Points |
|---|---|---|---|---|---|---|---|
| 1 |
 Tartu FC Merkuur |
26 | 18 | 4 | 4 | 52 | 58 |
| 2 |
 Jõhvi FC Lokomotiv |
26 | 15 | 7 | 4 | 35 | 52 |
| 3 |
 Lasnamäe FC Ajax |
26 | 15 | 6 | 5 | 16 | 51 |
| 4 |
 Narva United FC |
26 | 13 | 6 | 7 | 27 | 45 |
| 5 |
 Tabasalu JK Charma |
26 | 12 | 7 | 7 | 10 | 43 |
| 6 |
 Tallinna FC Levadia III |
26 | 12 | 5 | 9 | 8 | 41 |
| 7 |
 Tallinna JK Dünamo |
26 | 12 | 4 | 10 | -1 | 40 |
| 8 |
 Võru JK |
26 | 9 | 7 | 10 | -2 | 34 |
| 9 |
 Tallinna JK Legion |
26 | 11 | 1 | 14 | -4 | 34 |
| 10 |
 Jõgeva SK Noorus-96 |
26 | 8 | 7 | 11 | 2 | 31 |
| 11 |
 Tartu FC Santos II |
26 | 8 | 4 | 14 | -10 | 28 |
| 12 |
 Tallinna JK Piraaja |
26 | 6 | 6 | 14 | -26 | 24 |
| 13 |
 Kuusalu JK Rada |
26 | 6 | 3 | 17 | -53 | 21 |
| 14 |
 Kiviõli FC Irbis |
26 | 3 | 1 | 22 | -54 | 10 |
