Starting off his career with Malmö FF in 1985, he went on to represent FC Zürich, Benfica, Napoli, Roma, and Rangers before retiring in 1999.

He also represented his country at the 1988 Summer Olympics, 1990 FIFA World Cup, as well as UEFA Euro 1992.

Born in Falköping and raised in Värnamo, Thern started his professional career in 1985 when he joined Malmö FF, where he stayed for four years, winning two Allsvenskan titles in 1986 and 1988.

That same year, he left for Benfica as part of a successful group of Scandinavian players that played there at the same time.

It consisted of Danish international Michael Manniche (1983–1987), as well as the Swedish "armada" of Mats Magnusson (1987–1992), Thern (1989–1992), Glenn Strömberg (1982–84) and Stefan Schwarz (1990–94).