The 2012–13 Bayer Leverkusen season is the 109th season in the club's football history. In 2012–13, the club plays in the Bundesliga, the top tier of German football. It is the clubs 34th season in this league, having been promoted from the 2. Bundesliga in 1979.

The club also takes part in the 2012–13 edition of the DFB-Pokal.

In Europe, the club has qualified for the 2012–13 edition of the UEFA Europa League where it will play Metalist Kharkiv, Rapid Wien and Rosenborg in Group K of the group stage.

In the 2011–12 season, Bayer Leverkusen finished fifth in the 2011–12 Bundesliga. Therefore, the club qualified for the 2012–13 Bundesliga, 2012–13 DFB-Pokal and 2012–13 Europa League.

Bayer Leverkusen rejected a bid for André Schürrle worth €25 million from Chelsea. Bayer Leverkusen has decided not to sell Schürrle because they were "unable to sign a replacement" because suitable replacements are "too expensive" and would be forced to sign "a weaker player" who is "overpriced". Leverkusen CEO Wolfgang Holzhäuser accused Bayern Munich coach of Jupp Heynckes "tapping up" Lars Bender. The club had rejected an "official" offer from Bayern Munich the previous week.

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