Mainly a central midfielder, Thon's 19-year professional career was solely associated to Schalke 04 and Bayern Munich, having amassed more than 500 official games and 100 goals for both combined.

Also during that season, he scored a hat-trick against Bayern Munich in the DFB-Pokal, in a 6–6 home thriller in the semi-final stage; the Bavarians eventually won the replay and the tournament.

In the summer of 1988, Thon signed with national giants FC Bayern Munich, as a replacement for Inter Milan-bound Lothar Matthäus.

During his second spell, he played almost exclusively as a sweeper and, in his third year, played in a total of 46 official games, helping his club to the season's UEFA Cup final, where he scored his attempt in the penalty shootout win against Inter (1–1 on aggregate); Schalke could only finish 12th in the domestic league, however.

Due to either injuries or run-ins with national team manager Berti Vogts, the player missed the 1994 World Cup and the Euro 1992 and 1996 tournaments, ending his 14-year international career with 52 caps (three goals).