Wagner was a journeyman striker for his playing career, playing primarily for Mainz 05, Darmstadt 98, FC Gütersloh, and Schalke 04. He also had short at Waldhof Mannheim, Eintracht Frankfurt and TSG Weinheim and Germania Pfungstadt. He enjoyed his best spell at Mainz scoring 19 times in his four years at the club. Former teammate and lifelong friend Jurgen Klopp recalled that "He wasn't very consistent, even if he does not want to hear it [...] He was a big talent, but not every day. He was very a young player when he came from Eintracht Frankfurt to Mainz, a very skilled boy, very quick, a good striker." He was part of the Schalke squad that won the 1997 UEFA Cup.