| Competition: | Slovenian Second League |
| Season: | 2008–09 |
| Winners: | Olimpija |
| Promoted: | Olimpija |
| Relegated: | Bonifika Zagorje |
| League Topscorer: | Dejan Burgar (16 goals) |
| Total Goals: | 431 |
| Prevseason: | 2007–08 |
| Nextseason: | 2009–10 |
The 2008–09 Slovenian Second League season started on 10 August 2008 and ended on 24 May 2009. Each team played a total of 26 matches.