| Competition: | 2. česká fotbalová liga |
| Season: | 2008–09 |
| Winners: | Bohemians 1905 |
| Promoted: | Bohemians 1905 Slovácko |
| Relegated: | HFK Olomouc Fulnek |
| League Topscorer: | Martin Jirouš (18) |
| Matches: | 240 |
| Total Goals: | 578 |
| Average Attendance: | 1,689 |
| Prevseason: | 2007–08 |
| Nextseason: | 2009–10 |
The 2008–09 Czech 2. Liga was the 16th season of the 2. česká fotbalová liga, the second tier of the Czech football league. Bohemians 1905 were promoted to the Czech First League as winners of the league. Second placed Čáslav decided not to promote and sold their license to Slovácko, who were promoted in their place.[1]
Promoted to Czech First League
Relegated to Moravian-Silesian Football League
Relegated to Bohemian Football League
Relegated from Czech First League
Promoted from Bohemian Football League
Promoted from Moravian-Silesian Football League
| Rank | Scorer | Club | Goals |
|---|---|---|---|
| 1 |  Martin Jirouš | Sokolov | 18 |
| 2 | Petr Faldyna | Jihlava | 13 |
| 3 | Martin Opic | Karviná | 12 |
| 4 | David Korčián | HFK Olomouc | 11 |
| Luděk Zelenka | Dukla Prague | 11 | |
| 6 | Jaroslav Diviš | 10 | |
| Milan Halaška | Opava | 10 | |
| 8 | Michal Dian | Čáslav | 9 |
| Pavel Dvořák | 9 | ||
| Miloslav Strnad | 9 |