| Slovenian Football Cup | |
| Year: | 1999–2000 |
| Num Teams: | 32 |
| Champions: | Olimpija (3rd title) |
| Runner-Up: | Korotan Prevalje |
| Matches: | 38 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Slovenian Football Cup was the ninth season of the Slovenian Football Cup, Slovenia's football knockout competition.
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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.
Olimpija won 3–2 on aggregate.