The Spain international has put pen to paper on a fresh contract with los Rojiblancos, making him the fourth player to commit himself to the club since last week
The 28-year-old moved to the Spanish capital in January 2011 from Osasuna and has since established himself as a Rojiblancos regular, clocking up 79 league appearances for Diego Simeone's men and scoring twice.
"First I want to thank the club and the coach for the confidence they have shown in me," he told Atleti's official website. "I am very proud to wear to wear this shirt for many more years."
Sporting director Jose Luis Perez Caminero added: "I am very satisfied that we have reached an agreement with Juanfran because he has become a very important player for us."
The news follows the announcement that youngsters Koke, Oliver Torres and Javier Manquillo have also been tied down to long-term contracts at the club.
The capital club resume their league campaign by hosting Almeria on Saturday on the back of the international break.