The 21-year-old has become a key component of the Basque outfit's success in recent seasons, helping the club to fourth place in 2013-14 and a UEFA Champions League qualification spot.
Muniain scored seven La Liga goals from midfield last season, his best return yet, and was also part of the team that made a run to the UEFA Europa League final in 2012, where they lost 3-0 to Atletico Madrid.
With his performances reportedly attracting attention from other clubs, Athletic confirmed on Thursday that Muniain's contract had been extended to 2017, with a minimum buy-out clause of €37.5million.
"Athletic Club and Iker Muniain have signed a renewal agreement by which the player will remain in the red and white until June 30, 2017," a statement on the club's official website read.
"The termination clause will be of €37.5million to €40m."