The 2003–04 Slovenian Third League was the 12th season of the Slovenian Third League, the third highest level in the Slovenian football system. * Factor Ježica defeated Korte in a promotion play-offs (0–4, 4–0, 4–1 (pen.)). * Šoštanj defeated Nafta Lendava in a promotion play-offs (2–0, 0–0), but they did not get the competition licence for the 2.SNL, so Nafta took their place.