The Spanish club this evening confirmed the Belgium international would return to the Vicente Calderon after a successful spell in the capital last season.
After being immediately loaned out by Chelsea following his arrival from Racing Genk, the 20-year-old established himself as first choice at Atletico as they finished fifth in the Primera Division and won the Europa League.
"Thibaut Courtois will next season play at Atletico Madrid after Atletico on Wednesday reached an agreement with Chelsea on transfer for a year," a statement on the Spanish club's official website read.
"The Belgian international goalkeeper played all of last season on loan playing in in 37 games in La Liga and 15 in the UEFA Europa League - a competition won in Bucharest on May 9."
Atletico also confirmed that defender Alvaro Dominguez would join Borussia Monchengladbach.
The 23-year-old Spain international, who is set to hold a press conference at the Vicente Calderon on Thursday lunchtime, has signed a five-year deal to join the German club after passing a medical.