The 1999–2000 season was the 96th season in the history of Bayer 04 Leverkusen and the club's 21st consecutive season in the top flight of German football.

In addition to the domestic league, Leverkusen participated in this season's editions of the DFB-Pokal, the UEFA Champions League, and the UEFA Cup.

Win Draw Loss Source: Competitions Source: DFB