| Competition: | Slovenian Third League |
| Season: | 2008–09 |
| Total Goals: | 1149 |
| League Topscorer: | Januš Štante (19 goals) |
| Prevseason: | 2007–08 |
| Nextseason: | 2009–10 |
The 2008–09 Slovenian Third League was the 17th season of the Slovenian Third League, the third highest level in the Slovenian football system.
| Club | Location | Stadium | 2007–08 position | |
|---|---|---|---|---|
| Čarda | Martjanci | ŠRC Martjanci | 1st, Pomurska | |
| Črenšovci | Črenšovci | Črenšovci Sports Park | 7th | |
| Dravinja | Slovenske Konjice | Dobrava Stadium | 6th | |
| Dravograd | Dravograd | Dravograd Sports Centre | 3rd | |
| Kovinar Štore | Štore | Na Lipi Stadium | 12th | |
| Malečnik | Malečnik | Berl Sports Centre | 5th | |
| Mons Claudius | Rogatec | Rogaška Slatina City Stadium | 2nd, Styrian | |
| Odranci | Odranci | ŠRC Odranci | 8th | |
| Paloma | Sladki Vrh | Sladki Vrh Sports Park | 11th | |
| Šampion | Celje | Olimp Stadium | 1st, Styrian | |
| Šmarje pri Jelšah | Šmarje pri Jelšah | Sports Park | 9th | |
| Šmartno 1928 | Šmartno Stadium | 2nd | ||
| Stojnci | Stojnci | Stojnci Sports Park | 10th | |
| Veržej | Veržej | Čistina Stadium | 4th |
| Club | Location | Stadium | 2007–08 position | |
|---|---|---|---|---|
| Adria | Miren | Pri Štantu Stadium | 11th | |
| Brda | Dobrovo | Vipolže Stadium | 7th | |
| Dob | Dob | Dob Sports Park | 12th | |
| Jadran | Dekani | Dekani Sports Park | 6th | |
| Kamnik | Kamnik | Stadion Prijateljstva | 1st, Ljubljana | |
| Korte | Korte | Malija Stadium | 10th | |
| Kranj | Kranj | Zarica Sports Park | 3rd | |
| Krka | Novo Mesto | Portoval | 10th, 2. SNL | |
| Radomlje | Radomlje | Radomlje Sports Park | 8th | |
| Sava | Kranj | Stražišče Sports Park | 1st, Carniolan | |
| Slovan | Kodeljevo Sports Park | 9th | ||
| Šenčur | Šenčur | Šenčur Sports Park | 2nd | |
| Tabor Sežana | Sežana | Rajko Štolfa Stadium | 1st, Littoral | |
| Tolmin | Tolmin | Brajda Sports Park | 4th |