The album was a recording of the Moroccan group the Master Musicians of Joujouka, in performance in their village, Jajouka, spelled "Joujouka" on the original album. Jones called the tracks "a specially chosen representation" of music played in the village during the annual week-long Rites of Pan Festival.
The album's music included songs meant for the village's "most important religious holiday festival, Aid el Kbir". The festival's ritual of dressing a young boy dressed as "Bou Jeloud, the Goat God" wearing the "skin of a freshly slaughtered goat", involved the child's running to "spread panic through the darkened village" as the musicians played with abandon. Gysin connected the ritual, performed to protect the village's health in the coming year, to the fertility festival of Lupercalia and the "ancient Roman rites of Pan"; he referred to the Bou Jeloud dancer as "Pan" and "the Father of Skins". This name stuck, leading to the reference to Pan in the album's title.
Jones, recording engineer George Chkiantz, and Gysin travelled to the village in 1968, accompanied by Hamri and Jones's girlfriend Suki Potier to record the musicians using a portable Uher recorder. Jones worked on the two-track recordings in London, adding stereo phasing, echo, and other effects. Jones edited the full-band selection to 14 minutes by "cross-phasing fragments of a work that runs to some ninety minutes in uncut form".
The album included three types of music: repetitive vocal chants "similar to those employed throughout Islam", flute and drum music featuring "several distinct melodic motifs and improvisations over a drone" played by two flutists and several drummers, and the full village orchestra's drum and horn music played to accompany the "frenzied dance of Bou Jeloud, a Moroccan Pan".
New York Times reviewer Robert Palmer reported that the call-and-response horn motifs are "handed down from generation to generation". Palmer, noting the "drumming rhythms are definitely African", paraphrased Gysin as connecting the musical origins to Spain, "from the Moorish courts of Cordova and Seville".
The cover illustration on the 1971 album was originally a painting by Mohamed Hamri depicting the master musicians with Brian Jones in the center. Jones edited the album and prepared the art work together with designer, Al Vandenburg. He put one of Hamri's son’s paintings on the inside cover. Jones finished producing the LP several months before his death in 1969.
Jones' ex-girlfriend Anita Pallenberg said that Jones had wanted to incorporate the Jajouka sound into the music of the Rolling Stones. In the Jean-Luc Godard movie Sympathy for the Devil, Rolling Stones drummer Charlie Watts is seen playing a Jajouka drum during a rehearsal.
In 1995, a controversial CD reissue of the album was issued. It was licensed from Allen Klein's Musidor by Point Music. A new 1990s photo of Bachir Attar, by his wife and manager American photographer Cherie Nutting, replaced Hamri's original painting of Brian Jones and the Master Musicians of Joujouka which Jones had chosen as his cover. It also included in a side bar a photo of the late Jones by Michael Cooper as well as further contemporary photos of and a "Bou Jeloud" dancer by Nutting. The CD's album title changed to "Brian Jones Presents The Pipes of Pan At Jajouka" to tie in with Bachir Attar's eponymous group "Master Musicians of Jajouka featuring Bachir Attar". The name Master Musicians of Jajouka was used on the Master Musicians of Joujouka's second album due to contact conflicts. While the original vinyl album consisted of "two untitled, unbroken LP sides", the reissue separated the songs into six tracks with titles.. The reissue cut the Master Musicians of Joujouka out of their rights and resulted in international protests at concerts by Bachir Attar in London, New York and San Francisco as well as Philip Glass concerts in London and elsewhere. Brion Gysin's original sleeve-notes were altered to remove all reference to the central role that Hamri played in introducing him to the music of the village. A Brion Gysin illustration decorated an essay by Paul Bowles in the liner notes.The CD's executive producers were Philip Glass, Kurt Munkacsi, and Rory Johnston.. Brian Jones was credited as producer. The multi-page booklet also included reminiscences and edited essays about the original band written by Brion Gysin, (who died in 1986 and therefore was not consulted), David Silver, Stephen Davis, William Burroughs, Brian Jones, and Bachir Attar.
The original village group, mentored by Hamri from the 1950s until his death in 2000, continued releasing records on Sub Rosa Records, using their original name, Master Musicians of Joujouka as used on the 1971 release and Mohamed Hamri's Tales of Joujouka.
In 1995 they launched an international campaign demanding their interest in their recording with Brian Jones be recognised and that the re-release be withdrawn from sale until their concerns were addressed. A group led by the second youngest son of Hadj Abdesalam Attar still perform under the name "Master Musicians of Jajouka featuring Bachir Attar", recording with the Rolling Stones on Steel Wheels in 1989. Led by Attar's son and self proclaimed successor, as band leader Bachir Attar, also released soundtrack recordings under the Jajouka name and album recordings under the name Master Musicians of Jajouka Featuring Bachir Attar in the 1990s and 2000s. According to Bachir Attar the master musicians of that early group were led by tribal chief Hadj Abdesalam Attar. Rikki Stein who managed the Master Musicians of Joujouka/ Master Musicians of Jajouka noted that in 1971 the leaders of the musicians were Mohamed Attar, known as Berdouz, who led the drummers and Mallim Fedal who led the pipers. This throws doubt on the claim that Hadj Abdelsalm Attar was leader, tribal or otherwise, in the late 1960s or early 1970s.
Ahmed El Attar is the current leader of the original Master Musicians of Joujouka.