Butt joined Bayer 04 Leverkusen on a free transfer in 2001, being the side's undisputed starter in the subsequent campaigns (he only missed one Bundesliga match in his first five seasons combined and added seven goals), and appeared in all the games (17) for a team that lost to Real Madrid in the 2001–02 UEFA Champions League final, scoring a penalty in a 3–1 home win against Juventus F.C. in the second group stage.