The 1999–2000 campaign was the 94th season in Atlético Madrid's history and their 65th season in La Liga, the top division of Spanish football.

It covers a period from 1 July 1999 to 30 June 2000.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Players may hold more than one non-FIFA nationality.

Third round Eightfinals Quarterfinals Semifinals First round Second round Third round