Juanfran has established himself as a key member of the Atletico side since arriving from Osasuna in January 2011.
The 28-year-old was thought to be a target for Arsenal during last January's transfer window and is reported to have turned down overtures from Arsene Wenger's side to stay at Atletico.
Right-back Juanfran was delighted to pledge his long-term future to Atletico.
"First I want to thank the club and the coach for the confidence they have shown in me," Juanfran told the club's official website.
"I am very proud to wear this shirt for many more years."