| Estonian Championship | |
| Year: | 1938–39 |
| Winners: | Estonia Tallinn (5th title) |
| Prev Season: | 1937–38 |
| Next Season: | 1939–40 |
The 1938–39 Estonian Top Division was the 18th official football league season in Estonia. JS Estonia Tallinn won the title.
| Pos | Name | Team | Goals |
|---|---|---|---|
| 1 | Osvald Kastanjan-Kastan | Tallinna Jalgpalliklubi | 13 |
| 2 | Johannes Niks | ESS Kalev Tallinn | 10 |
| 3 | Richard Kuremaa | JS Estonia Tallinn | 8 |
| 4 | Ralf Veidmann | ESS Kalev Tallinn | 7 |
| Otto Lõhmus | PK Olümpia Tartu | 7 | |
| Heinrich Uukkivi | JS Estonia Tallinn | 7 |