The 2006 Esiliiga is the 16th season of the Esiliiga, second-highest Estonian league for association football clubs, since its establishment in 1992.
FC Kuressaare gained automatic promotion to the Meistriliiga as FC Levadia II are the reserve team for Meistriliiga champions FC Levadia and therefore can not be promoted to the same league as its parent club. JK Tallinna Kalev also go up after winning the promotion-relegation play-off.The league's top-scorer was FC Levadia youngster Kaimar Saag with 37 goals. Nõmme Kalju's Andrus Mitt scored 35 goals.
As of 11 November 2007.[1]
| Rank | width=175px | Player | width=100px | Club | Goals |
|---|---|---|---|---|---|
| 1 |  Kaimar Saag | Levadia II | 37 | ||
| 2 | Andrus Mitt | Nõmme Kalju | 35 | ||
| 3 | Jevgeni Gurtšioglujants | Levadia II | 17 | ||
| Sander Puri | Levadia II | 17 | |||
| 5 | Artjom Dmitrijev | TVMK II | 16 | ||
| Tiit Tikenberg | Tallinna Kalev | 16 | |||
| 7 | Dmitri Kirilov | Tallinna Kalev | 15 | ||
| 8 | Kristian Marmor | Levadia II | 14 | ||
| 9 | Eino Puri | Levadia II | 12 | ||
| Anton Semjonov | Lootus | 12 | |||
| Rainer Veskimäe | Kuressaare | 12 | |||