| Competition: | 2. česká fotbalová liga |
| Season: | 2006–07 |
| Winners: | Viktoria Žižkov |
| Promoted: | Viktoria Žižkov Bohemians 1905 |
| Relegated: | Sigma Olomouc "B" Dosta Bystrc Jakubčovice Blšany |
| League Topscorer: | Petr Faldyna (15) |
| Matches: | 240 |
| Total Goals: | 577 |
| Average Attendance: | 1,467 |
| Prevseason: | 2005–06 |
| Nextseason: | 2007–08 |
The 2006–07 Czech 2. Liga was the 14th season of the 2. česká fotbalová liga, the second tier of the Czech football league.
Promoted to Czech First League
Relegated to Moravian-Silesian Football League
Relegated to Bohemian Football League
Relegated to Divize E
Relegated to 5. Liga (Pardubický kraj)
Relegated
Folded
Relegated from Czech First League
Promoted from Bohemian Football League
Promoted from Moravian-Silesian Football League
Promoted from Divize B
Promoted from 5. Liga (Moravskoslezský kraj)
| Rank | Scorer | Club | Goals |
|---|---|---|---|
| 1 |  Petr Faldyna | Jihlava | 15 |
| 2 | Petr Fousek | Ústí nad Labem | 9 |
| Ivo Svoboda | Jihlava | 9 | |
| Petr Švancara | Viktoria Žižkov | 9 | |
| 5 | Vladimír Bálek | Bohemians 1905 | 8 |
| Miroslav Černý | Vítkovice | 8 | |
| Martin Hanus | Hlučín | 8 | |
| Libor Kozák | Opava | 8 | |
| Jan Novotný | Viktoria Žižkov | 8 | |
| Michal Salák | Sokolov | 8 | |
| Dalibor Slezák | Bohemians 1905 | 8 |