Soon after arriving back in Massachusetts, Thompson dropped out of college, and moved to Boston with Santiago. He spent 1984 working in a warehouse, "managing buttons on teddy bears", composing songs on his
acoustic guitar, and writing lyrics on the
subway train. In January 1985, Thompson formed the Pixies with Santiago. Bassist
Kim Deal was recruited a week later via a classified advert placed in a Boston paper, which requested a bassist "into
Hüsker Dü and
Peter, Paul and Mary," and joined a week later. Drummer
Dave Lovering was later hired on recommendation from Deal's husband.
In 1987, the Pixies recorded an eighteen-track
demo tape, commonly referred to as
The Purple Tape amongst fans. Thompson's (natural) father assisted the band financially, loaning $1000 in order to record the demo tape; Thompson later said that his father "wasn't around for a lot of my younger years, so I think he was doing his best to make up for lost time".
The Purple Tape led to a recording contract with the English independent record label
4AD. Thompson adopted the alias "Black Francis" for the release of
Come on Pilgrim, a name inspired by his father: “he had been saving that name in case he had another son”.
In 1988, the Pixies recorded their second album
Surfer Rosa. Francis wrote and sang on all the tracks, with the exception of the single "
Gigantic", which was co-written and sung by Deal. To support the album, the band undertook a European tour, during which Francis met
Eric Drew Feldman, a later collaborator on Pixies and solo albums.
Doolittle, with Francis-written songs such as "Debaser" and "Monkey Gone To Heaven", was released the following year to widespread critical acclaim. However, by this time, tensions between Francis and Deal combined with exhaustion, and led the band to announce a hiatus. Francis has an aversion to flying, and spent this time driving across America with his girlfriend, Jean Walsh (whom Francis had met in the band's early days), performing solo shows in order to raise funds to buy furniture for his new
Los Angeles apartment.
The band reconvened in 1990, and recorded two further albums: 1990s
Bossanova and 1991's
Trompe le Monde; the latter was Francis' first collaboration with Feldman. The later Pixies albums were characterized by Francis' increasing influence on the band's output, as well as a focus on
science fiction themes, including
aliens and
UFOs. These themes would continue to be explored throughout his early solo work.
Trompe le Monde includes the song "U-Mass", which was written about the university he attended as a youth, and due to the keyboard part played by Feldman, signified a move away from the band's purely alternative rock sound. Although Deal had contributed to previous albums, from
Bossanova on, Francis wrote all the band's original material. This contributed to the increasing tension between Francis and Deal, and the Pixies broke up in 1992; this was not publicly announced until early in 1993.