1999–2000 Slovenian Football Cup

The 1999–2000 Slovenian Football Cup was the ninth season of the Slovenian Football Cup, Slovenia's football knockout competition.

1998–99 Slovenian PrvaLiga members

 * Beltinci
 * Celje
 * Domžale
 * Gorica
 * Koper
 * Korotan Prevalje
 * Maribor
 * Mura
 * Olimpija
 * Primorje
 * Rudar Velenje
 * Triglav Kranj

Qualified through MNZ Regional Cups

 * MNZ Ljubljana: Elan, Factor, Ivančna Gorica
 * MNZ Maribor: Železničar Maribor, Paloma, Pohorje
 * MNZ Celje: Šentjur, Šmartno
 * MNZ Koper: Tabor Sežana, Ilirska Bistrica
 * MNZ Nova Gorica: Idrija, Brda
 * MNZ Murska Sobota: Veržej, Tromejnik
 * MNZ Lendava: Odranci, Črenšovci
 * MNZG-Kranj: Lesce, Britof
 * MNZ Ptuj: Drava Ptuj, Aluminij

First round

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Quarter-finals
Olimpija won 6–2 on aggregate.

Korotan won 3–0 on aggregate.

Gorica won 5–4 on aggregate.

Maribor won 5–2 on aggregate.

Semi-finals
Korotan Prevalje won 4–3 on aggregate.

Olimpija won 3–2 on aggregate.

Final
Olimpija won 3–2 on aggregate.