The 1998–99 Macedonian Football Cup was the 7th season of Macedonia's football knockout competition. Vardar defended their title, having won their fourth title.
Competition calendar
Source:
First round
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Sources:
Group stage
The most results are unknown.
Group 1
Pobeda and Vardar were advanced to the quarterfinal, the other teams in group were Kumanovo and Sasa.
Group 2
Group 3
Group 4
Sileks and Osogovo were advanced to the quarterfinal, the other teams in group were Pelister and Ilinden Skopje.
Sources:
Quarter-finals
The first legs were played on 10 March and second were played on 17 March 1999.
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Semi-finals
The first legs were played on 7 April and the second were played on 21 April 1999.