Thon returned to his first club Schalke in 1994, at the age of 28, after winning another league title, although he spent most of the season injured and Matthäus had already returned to Bayern. 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.