| Competition: | Macedonian Second League |
| Season: | 2003–04 |
| Winners: | Bregalnica Shtip |
| Promoted: | Bregalnica Shtip Shkëndija Tetovo |
| Relegated: | Borec Novaci Osogovo Alumina Lozar Kumanovo 11 Oktomvri Zletovica |
| Prevseason: | 2002–03 |
| Nextseason: | 2004–05 |
The 2003–04 Macedonian Second Football League was the twelfth season since its establishment. It began on 9 August 2003 and ended on 2 June 2004.[1]