Muller played as a lock for the Sharks (Currie Cup), Sharks in (Super Rugby) and his country's national side Springboks, before he moved to Northern Ireland to play with Ulster in 2010, where became team captain, before retiring at the end of the 2013–2014 season.

Muller was selected into the Springboks squad for the 2007 home tests and the 2007 Tri Nations on the basis of a strong 2007 Super 14 performance.

During the latter part of the competition, Springbok coach Jake White decided to rest his top players from touring Australia and New Zealand.

[1] White stated that the players that were taken on this tour would be playing for places in the Springboks 2007 Rugby World Cup squad.

Johann Muller joined Ulster Rugby in 2010, where his solid performances saw him selected as the captain of the team.