Müller began his football career by making his way through the youth ranks at FC Bayern Munich, in Germany. The 2008-2009 season was a big one for Müller, as he was a core member of the Bayern II team in the 3rd Liga in Germany, scoring 15 goals. That led to him making his debut for the senior side in 2008, against Hamburg. The young attacking midfielder and striker made five appearances that season, scoring his maiden goal in the Champions League against Sporting.
The following season, Müller expected to be sent on loan for first-team football; however new manager Louis van Gaal kept him in the Bayern squad, where he eventually became a regular in the side. Müller played in nearly every game for Bayern, scoring 19 times in all competitions as they won the domestic double and fell just short of a remarkable treble – losing to Inter Milan 2-0 in the Champions League final. Müller would back up his breakthrough season the next year, with another 19 goals in 2010-2011.
Müller's moment to shine came at the 2010 FIFA World Cup in South Africa. He had represented Germany at various youth levels, and prior to the tournament he had made his debut in a friendly against Argentina in early 2010. But Müller's performance on the big stage was sensational, winning the Golden Boot with five goals as Germany were third overall, and won the Best Young Player award.