The band was formed in 1998 by childhood friends José González and Elias Araya along with Tobias Winterkorn. The group was formed as a hobby for the three, who at the time held other occupations: Winterkorn was a part-time teacher, Araya an art student and González was studying biochemistry. In 2000 they released their first EP, Straight Lines.
The band was put on hold when, in 2003, González's solo career took off, at which time he left his studies and started touring. In 2005, the band released their second EP, Black Refuge, after which González again embarked on a solo tour.
The band released their first full-length album, Fields, in 2010. On its subsequent tour, the band's live lineup was expanded to include bass and percussion. Three years later, Junip released their self-titled second album. After the recording of the album and before going on its supporting tour, Araya left the band, being replaced on live performances by other drummers.