The 2003–04 Macedonian Football Cup was the 12th season of Macedonia's football knockout competition.
Cementarnica 55 were the defending champions, having won their first title.
The 2003–04 champions were Sloga Jugomagnat who won their third title after appearing in their eighth Final in nine seasons.
The first legs were played on 10 March and the second on 15 April 2004.
Sloga Jugomagnat won on away goals.