The 1999–2000 Slovenian Football Cup was the ninth season of the Slovenian Football Cup, Slovenia's football knockout competition.
Olimpija won 6–2 on aggregate.
Korotan won 3–0 on aggregate.
Gorica won 5–4 on aggregate.
Maribor won 5–2 on aggregate.
Korotan Prevalje won 4–3 on aggregate.
Olimpija won 3–2 on aggregate.