The 1999–2000 FC Bayern Munich season was the 100th season in the club's history.

FC Bayern Munich clinched its second consecutive league title, its third consecutive DFB-Ligapokal championship, and the 1999–2000 DFB-Pokal.

Source: KickerOnly competitive matches = Number of bookings; = Number of sending offs after a second yellow card; = Number of sending offs by a direct red card.

Total spending: €16,550,000

Total income: €3,450,000 The 1999–2000 Bundesliga campaign began on 14 August when Bayern played in the opening game of the season against Hamburg.