| Competition: | Slovenian Second League |
| Season: | 2003–04 |
| Winners: | Rudar Velenje |
| Promoted: | Bela Krajina Zagorje |
| League Topscorer: | Ismet Ekmečić (30 goals) |
| Total Goals: | 562 |
| Prevseason: | 2002–03 |
| Nextseason: | 2004–05 |
The 2003–04 Slovenian Second League season started on 10 August 2003 and ended on 6 June 2004. Each team played a total of 32 matches.