| Competition: | Slovenian Second League |
| Season: | 2006–07 |
| Winners: | Livar |
| Relegated: | Šenčur Dravinja |
| League Topscorer: | Dejan Božičič Dalibor Volaš (14 goals) |
| Matches: | 135 |
| Total Goals: | 358 |
| Prevseason: | 2005–06 |
| Nextseason: | 2007–08 |
The 2006–07 Slovenian Second League season started on 13 August 2006 and ended on 27 May 2007. Each team played a total of 27 matches.