PFR was founded in 1989 as the Joel Hanson Band by Joel Hanson, who was a camp counselor at Camp Shamineau, a Christian youth camp in Minnesota. In 1991, the band, known then as Inside Out, was signed to Brown Bannister's newly founded Vireo Records. After signing, Patrick Andrew suggested the band change the name to Pray For Rain after a line from a poem. Later, they settled on the name PFR. In 1992, the band released the album Pray For Rain, and gained some attention with the song "Do You Want To Know Love".

In 1993, PFR released their second album, Goldie's Last Day, whose title track was inspired by the passing of Patrick Andrew's pet golden retriever. Also that year, the band recorded a cover of "We Can Work It Out" by The Beatles with guitar legend Phil Keaggy for the various artists tribute CD Come Together: America Salutes The Beatles.

PFR released their third album, Great Lengths in 1994. The album had the band's biggest hit, "The Love I Know," inspired by 1 Corinthians 13. Having changed musical direction with each album, PFR moved into an edgier, heavy sound for 1996's Them. While the album was well-received, the band shortly afterward announced that they were splitting up. In 1997, The Late Great PFR was released, a greatest hits album containing three new songs, with one ("Forever") becoming a Christian radio hit.

Over the next 5 years, the band reunited for an occasional benefit concert. In 2000, when Mark Nash was working as the A&R director of Squint Records, the band returned to the studio to contribute to Steve Taylor's Roaring Lambs project, inspired by the book by Bob Briner. Working on the project inspired the band to sign to Taylor's Squint Records, and record 2001's Disappear.

PFR returned in 2004 with a new full-length release, The Bookhouse Recordings, an album chiefly consisting of PFR classics rearranged, plus three new songs. The Bookhouse Recordings was recorded in one week at the end of August 2004 in Nashville, TN at Mark Nash's studio. This was the first album wholly produced by the band alone, and features the song "Prayer For Beslan," a song mourning the terrorist attacks on a Russian school the same week the band was recording.

In 2012, PFR reunited once again for the "PFR Twelve In 2012" tour. In December 2012, PFR released a 13-track, live album entitled Minneapolis. The band once again disbanded in 2013.