The 1998–99 FR Yugoslavia Cup was the seventh season of the FR Yugoslavia's annual football cup.
The cup defenders was FK Partizan, but was defeated by Red Star Belgrade in the final.
Thirty-two teams entered in the First Round.
Note: Roman numerals in brackets denote the league tier the clubs participated in the 1998–99 season.
Note: Roman numerals in brackets denote the league tier the clubs participated in the 1998–99 season.