After an excellent season in which they won La Liga and reached the Champions League final, the pair were linked to moves away from the club, with several Premier League sides expressing an interest in them.
However, the players have shrugged off offers from other clubs - with midfielder Koke most notably linked with Barcelona and Chelsea - and opted to stay at the Vicente Calderon.
The club have confirmed that Koke, 22, and right-back Juanfran, 29, will remain in the Spanish capital, having signed new five and four year deals respectively.
"Koke and Juanfran have extended their contracts with our club until 2019 and 2018," an Atleti statement read.
"Both players are key pieces of Atletico's recent success and their renewals are great news for the club.
"Koke started in our youth ranks and has become one of the stalwarts of the current Atletico Madrid team. He was a key part in the league and cup titles won in the last two seasons.
"Meanwhile, Juanfran joined in the winter of the 2010-11 season from Osasuna and has established himself as one of the best right-backs in the league and in Europe in the last three campaigns."