The Spain internationals were central figures as Atleti claimed their first Liga title since 1996 last term, while they were also involved in the club's run to the UEFA Champions League final, where Diego Simeone's side lost to city rivals Real Madrid in extra time.
Koke, 22, came through the youth ranks at Vicente Calderon and has made 169 appearances for the club, scoring 13 goals. He has extended his stay at the club until 2019.
Juanfran, meanwhile, has been in the Spanish capital since joining from Osasuna in 2011.
The 29-year-old has since made 161 outings for Atletico and has been rewarded with an extension, until 2018.
In addition to the 2013-14 league title, the duo have tasted victory in the UEFA Europa League, UEFA Super Cup and Copa del Rey during their time with the club.
Both were part of the Spain squad for the 2014 FIFA World Cup, but the reigning champions' defence was ended in the group stages.