The 1998–99 FC Bayern Munich season was the 99th season in the club's history.

Bayern Munich played in the dramatic 1999 UEFA Champions League Final against Manchester United.

[1] Bayern Munich dominated the match, taking the lead through a Mario Basler free-kick and hitting the woodwork twice, before United substitutes Teddy Sheringham and Ole Gunnar Solskjær scored in injury time to win the treble for the English side.

[1] Win Draw Loss Postponed

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.