| Macedonian Football Cup | |
| Year: | 1999–00 |
| Dates: | 15 September 1999 – 20 May 2000[1] |
| Num Teams: | 32 |
| Defending Champions: | Vardar |
| Champions: | Sloga Jugomagnat (2nd title) |
| Runner-Up: | Pobeda |
| Matches: | 76 |
| Goals: | 306 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Macedonian Football Cup was the 8th season of Macedonia's football knockout competition. Vardar were the defending champions, having won their fourth title. The 1999–2000 champions were Sloga Jugomagnat who won their second title.
| Round | Date(s) | Fixtures | Clubs | New entries |
|---|---|---|---|---|
| First Round | 15 September 1999 | 16 | 32 → 16 | 32 |
| Group stage | 22, 29 September, 20 October, 10, 28 November 1999 & 27 February 2000 | 48 | 16 → 8 | none |
| Quarter-finals | 15, 22 March 2000 | 8 | 8 → 4 | none |
| Semi-finals | 5, 19, 20 April 2000 | 4 | 4 → 2 | none |
| Final | 20 May 2000 | 1 | 2 → 1 | none |
Source:[2]
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The first legs were played on 15 March and second were played on 22 March 2000.
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The first legs were played on 5 April and the second were played on 19 and 20 April 2000.
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Pobeda won 4–3 on aggregate.----
Sloga Jugomagnat won 4–2 on aggregate.