The Spanish teams also met in the 2014 final, with Real winning both times.
The draw on Friday pitted Juventus and Monaco in the other semifinal.
Real and Monaco will play the first legs at home, with one game on May 2 and another on May 3.
The return legs will be the following week.
The Madrid clubs have faced each other in the last three Champions Leagues. Real also defeated Atletico in the 2015 quarterfinals.
In its seventh straight semifinal, Real is trying to become the first team to repeat as champion since the competition's new format was created in 1992. It won a record-extending 11th title last season.
Atletico is seeking its first title. In addition to the defeats against Real, it also lost to Bayern Munich in the 1974 final.
Two-time champion Juventus is trying to return to the final since losing the final to Barcelona in 2015. That year, it eliminated Monaco in the quarterfinals with a 1-0 aggregate score.
The Italian champion is looking for its first European title since 1996.
Monaco is in the semifinals for the first time since it lost the 2004 final to FC Porto.
The final is in Cardiff on June 3.