The keeper signed for Chelsea from Belgian club Genk on Monday for a reported €9m (£7.9m).
A statement on the Atletico Madrid website said: "Atletico Madrid and Chelsea have reached an agreement for the transfer of Belgian goalkeeper Thibaud Courtois for next season.
"The 19-year-old goalkeeper passed a medical on Friday morning and signed the contract with his new club. On Sunday, he will train with Atletico for the first time."
The loan completes Atletico's hunt for a new goalie following David de Gea's move to Manchester United this summer.