| Competition: | Meistriliiga |
| Season: | 2003 |
| Winners: | Flora 7th title |
| Relegated: | Kuressaare |
| Continentalcup1: | Champions League |
| Continentalcup1 Qualifiers: | Flora |
| Continentalcup2: | UEFA Cup |
| Continentalcup2 Qualifiers: | TVMK Levadia Maardu |
| Continentalcup3: | Intertoto Cup |
| Continentalcup3 Qualifiers: | Narva Trans |
| League Topscorer: | Tor Henning Hamre (39) |
| Total Goals: | 423 |
| Matches: | 140 |
| Prevseason: | 2002 |
| Nextseason: | 2004 |
The 2003 Meistriliiga was the 13th season of the Meistriliiga, the top Estonian league for association football clubs, since its establishment in 1992.
Flora won their 7th Meistriliiga title.
Valga won 5–2 on aggregate and retained their Meistriliiga spot for the 2004 season.
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 |  Tor Henning Hamre | Flora | 35 |
| 2 |  Andrei Krõlov | TVMK | 22 |
| 3 | Ingemar Teever | TVMK | 21 |
| 4 | Maksim Gruznov | Narva Trans | 16 |
| 5 | Argo Arbeiter | Levadia Maardu | 14 |
| Vjatšeslav Zahovaiko | Flora | ||
| 7 |  Dmitri Lipartov | Narva Trans | 12 |
| Vladimir Tšelnokov | Levadia Maardu | ||
| 9 | Enver Jääger | Tulevik | 11 |
| Maksim Rõtškov | Levadia Maardu | ||
| Kristen Viikmäe | Flora |