| Season | 1999 |
|---|---|
| Champions | Levadia (1st title) |
| Top goalscorer | Toomas Krõm (19) |
← 1998 2000 → | |
The 1999 Meistriliiga was the ninth season of the Meistriliiga, Estonia's premier football league. Levadia won their first title.
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Qualification or relegation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Levadia (C) | 28 | 23 | 4 | 1 | 77 | 12 | +65 | 73 | Qualification for Champions League first qualifying round |
| 2 | Tulevik | 28 | 16 | 5 | 7 | 57 | 34 | +23 | 53 | Qualification for UEFA Cup qualifying round |
| 3 | Flora | 28 | 13 | 8 | 7 | 60 | 33 | +27 | 47 | |
| 4 | Narva Trans | 28 | 11 | 7 | 10 | 40 | 28 | +12 | 40 | Qualification for Intertoto Cup first round |
| 5 | TVMK | 28 | 7 | 9 | 12 | 16 | 33 | −17 | 30 | |
| 6 | Lantana | 28 | 6 | 9 | 13 | 31 | 52 | −21 | 27 | |
| 7 | Lelle | 28 | 5 | 9 | 14 | 25 | 45 | −20 | 24 | Qualification for relegation play-offs |
| 8 | Eesti Põlevkivi Jõhvi (R) | 28 | 2 | 7 | 19 | 12 | 81 | −69 | 13 | Relegation to Esiliiga |
Lelle won 4–2 on aggregate and retained their Meistriliiga spot; however, Lelle ceded their league entry to FC Valga both being associate clubs of Flora
Each team played every opponent four times, twice at home and twice on the road, for a total of 36 games.
| Rank | Player | Club | Goals[1] |
|---|---|---|---|
| 1 |  Toomas Krõm |
Levadia | 19 |
| 2 | Andrei Krõlov |
Levadia | 18 |
| 3 | Dmitri Ustritski |
Tulevik | 16 |
| 4 | Vitali Leitan |
Lantana | 15 |
| 5 | Indrek Zelinski |
Flora | 14 |
| 6 | Maksim Gruznov |
Narva Trans | 13 |
| 7 | Kristen Viikmäe |
Flora | 12 |
| 8 | Aleksandr Marašov |
Narva Trans | 10 |
| 9 | Konstantin Kolbasenko |
Levadia | 9 |
| 10 | Indro Olumets |
Levadia | 8 |