League standings
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Promotion or relegation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | FC Levadia II[a] (C) | 36 | 22 | 6 | 8 | 83 | 33 | +50 | 72 | |
| 2 | FC Kuressaare (P) | 36 | 21 | 8 | 7 | 67 | 35 | +32 | 71 | Promotion to Meistriliiga |
| 3 | FC Flora II[a] | 36 | 18 | 8 | 10 | 62 | 41 | +21 | 62 | |
| 4 | FC Flora Paide LM | 36 | 14 | 11 | 11 | 58 | 44 | +14 | 53 | Qualification for promotion play-offs |
| 5 | Valga Warrior | 36 | 13 | 9 | 14 | 46 | 56 | −10 | 48 | |
| 6 | Kiviõli Tamme Auto | 36 | 11 | 11 | 14 | 51 | 66 | −15 | 44 | |
| 7 | JK Maag Tammeka II[a] | 36 | 11 | 10 | 15 | 60 | 63 | −3 | 43 | |
| 8 | FC Flora Rakvere | 36 | 10 | 7 | 19 | 53 | 82 | −29 | 37 | |
| 9 | Lasnamäe Ajax | 36 | 8 | 9 | 19 | 59 | 79 | −20 | 33 | Qualification for relegation play-offs |
| 10 | FC TVMK II[b] (R) | 36 | 11 | 3 | 22 | 58 | 98 | −40 | 36 | Relegation to II liiga |
- ^ a b c Reserve teams are ineligible for promotion.
- ^ On 6 November Estonian Football Association License Commission decided to take TVMK's license to play in Meistriliiga or Esiliiga, due to financial difficulties during the season. The Estonian Football Association helped them to play until the end of the season and as they finished in 3rd place, the players and coaches got bronze medals, but the club itself was demoted to 10th spot.[1][2][3]
Relegation play-off
Ajax Lasnamäe and II Liiga Ida/Põhi side TJK Legion will compete in a two-legged relegation play-off for one spot in 2009 Esiliiga.
| TJK Legion | 2 – 0 | Ajax Lasnamäe |
|---|---|---|
Kisseljov  2'Kutuzov 77' |
Report |
| Ajax Lasnamäe | 1 – 1 | TJK Legion |
|---|---|---|
| Kirpu 3' |
Report | Kisseljov 67' |
