From 1 July 2001, Toppmöller was coach with Bayer 04 Leverkusen, whom in his first season led to the UEFA Champions League final, as well as second place in Bundesliga and the DFB-Pokal final. Toppmöller was eventually declared by German sports journalists as "football coach of the year" for 2002. However, in the following season Leverkusen performed poorly, and in light of a poor league position which could have led to relegation, Toppmöller was sacked on 16 February 2003.