The 1998–99 season was the 53rd season in FK Partizan's existence.

This article shows player statistics and matches that the club played during the 1998–99 season.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Players may hold more than one non-FIFA nationality.

The championship was stopped on 14 May 1999, because of the NATO bombing of Yugoslavia, after 24 rounds.