On 1 July 2009, Van Gaal took over as coach of Bayern Munich.
He referred to his new employer as a "dream club".
On 28 August 2009, he strengthened his team by signing compatriot Arjen Robben from Real Madrid; this reunited the two, with Van Gaal selecting Robben for his debut in the Netherlands U20 team.

Van Gaal got off to a poor start as Bayern coach, winning only one of his first four matches in charge, and by November the club was on the brink of a Champions League group stage exit following two losses to Bordeaux.
With Bayer Leverkusen at the top of the Bundesliga, speculation was rampant that he was on the brink of a departure from Bayern even earlier than his predecessor Jürgen Klinsmann.
Van Gaal, however, kept insisting he is a "prozesstrainer", meaning that his team needs time to play the way he imagines.

Van Gaal installed many youth players as fixtures in the starting 11, including Thomas Müller and Holger Badstuber, and also converted the winger Bastian Schweinsteiger into a defensive midfielder.
A feud with Italian striker Luca Toni, who had played an important role in Bayern's 2007–08 league and cup double, led to Toni's move to Roma.
Bayern Munich's form, however, improved with two Champions League victories including an impressive 4–1 victory over Juventus in Turin, which allowed them to progress from their group in second position behind Bordeaux.
By March, Bayern had moved to the semi-finals of the DFB-Pokal and were top of the Bundesliga, ahead of Bayer Leverkusen.

On 8 May 2010, Bayern were crowned Bundesliga champions following a 3–1 win at Hertha BSC, making Van Gaal the first ever Dutch coach to win the Bundesliga.
On 15 May 2010, Bayern won the DFB-Pokal with a 4–0 victory over Werder Bremen, thus securing the domestic double.

In the Champions League, Bayern won 4–4 on the away goals rule in the quarter-final against Manchester United and 4–0 on aggregate against Lyon in the semi-final, securing them a spot in the final, where Van Gaal was to meet his former pupil and assistant at Barcelona, Internazionale coach José Mourinho.
Bayern, however, lost the final 2–0, handing Inter a first Italian treble and thus failing to secure the treble themselves.
On 25 May 2010, Karl-Heinz Rummenigge expressed his desire to extend Van Gaal's contract as the club was very happy with his performance, despite Van Gaal still having one year of his contract to fulfil.
At the end of the season, Van Gaal was voted Manager of the Year by the German professional footballers in the yearly poll organized by VDV (professional players' union in Germany) and kicker.

Van Gaal's Bayern started the 2010–11 season by winning the DFL-Supercup, which had been officially reinstated after a 14-year absence.

On 7 March 2011, Bayern Munich declared that Van Gaal's contract was to be cancelled after the end of the 2010–11 season.
However, he was instead sacked on 10 April 2011 after losing the third place in the Bundesliga.
On 1 July 2009, Van Gaal took over as coach of Bayern Munich. He referred to his new employer as a "dream club". On 28 August 2009, he strengthened his team by signing compatriot Arjen Robben from Real Madrid; this reunited the two, with Van Gaal selecting Robben for his debut in the Netherlands U20 team.
Van Gaal got off to a poor start as Bayern coach, winning only one of his first four matches in charge, and by November the club was on the brink of a Champions League group stage exit following two losses to Bordeaux. With Bayer Leverkusen at the top of the Bundesliga, speculation was rampant that he was on the brink of a departure from Bayern even earlier than his predecessor Jürgen Klinsmann. Van Gaal, however, kept insisting he is a "prozesstrainer", meaning that his team needs time to play the way he imagines.
Van Gaal installed many youth players as fixtures in the starting 11, including Thomas Müller and Holger Badstuber, and also converted the winger Bastian Schweinsteiger into a defensive midfielder. A feud with Italian striker Luca Toni, who had played an important role in Bayern's 2007–08 league and cup double, led to Toni's move to Roma. Bayern Munich's form, however, improved with two Champions League victories including an impressive 4–1 victory over Juventus in Turin, which allowed them to progress from their group in second position behind Bordeaux. By March, Bayern had moved to the semi-finals of the DFB-Pokal and were top of the Bundesliga, ahead of Bayer Leverkusen.
On 8 May 2010, Bayern were crowned Bundesliga champions following a 3–1 win at Hertha BSC, making Van Gaal the first ever Dutch coach to win the Bundesliga. On 15 May 2010, Bayern won the DFB-Pokal with a 4–0 victory over Werder Bremen, thus securing the domestic double.
In the Champions League, Bayern won 4–4 on the away goals rule in the quarter-final against Manchester United and 4–0 on aggregate against Lyon in the semi-final, securing them a spot in the final, where Van Gaal was to meet his former pupil and assistant at Barcelona, Internazionale coach José Mourinho. Bayern, however, lost the final 2–0, handing Inter a first Italian treble and thus failing to secure the treble themselves. On 25 May 2010, Karl-Heinz Rummenigge expressed his desire to extend Van Gaal's contract as the club was very happy with his performance, despite Van Gaal still having one year of his contract to fulfil. At the end of the season, Van Gaal was voted Manager of the Year by the German professional footballers in the yearly poll organized by VDV (professional players' union in Germany) and kicker.
Van Gaal's Bayern started the 2010–11 season by winning the DFL-Supercup, which had been officially reinstated after a 14-year absence.
On 7 March 2011, Bayern Munich declared that Van Gaal's contract was to be cancelled after the end of the 2010–11 season. However, he was instead sacked on 10 April 2011 after losing the third place in the Bundesliga.
Louis van Gaal