| Competition: | Meistriliiga |
| Season: | 1999 |
| Winners: | Levadia (1st title) |
| League Topscorer: | Toomas Krõm (19) |
| Prevseason: | 1998 |
| Nextseason: | 2000 |
The 1999 Meistriliiga was the ninth season of the Meistriliiga, Estonia's premier football league. Levadia won their first title.
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 |