Thompson studied in the University of Massachusetts, before taking off to Puerto Rico as part of an exchange program. It was here where he reportedly spent six months in an apartment with a "weird, psycho, gay room mate." His insufficient grasp of the local language (which meant he couldn't even open a bank account to cash his cheques) forced him to make a decision whilst slumped in a local bar. He would either go to New Zealand to observe the passing of Halley's Comet or form a rock band.
After the split (due to internal tensions between Black Francis and Kim Deal) of the Pixies, he went on to record solo material with Eric Drew Feldman, and started a new band, Frank Black and the Catholics, in the late 1990s. He enjoys moderate solo success, although not at the level the Pixies attained.
In late 2003, rumors were spreading again that the Pixies were reuniting. The official announcements were made that the band was, in fact, practicing for a reunion tour. They played publicly again for the first time in April 2004, after a break of 12 years, and went on to tour extensively in the USA, Canada and Europe in the same year.