 Thom made his historic debut for his new club on 17 February 1990, and scored the opening goal in a 3–1 win over FC Homburg.Thom spent over five years at Bayer Leverkusen, and picked up a winner's medal on 12 June 1993 win they defeated Hertha BSC II 1–0 in the final of the DFB-Pokal.Thom signed for Glasgow club Celtic in July 1995 for a then club record fee of £2.2million.