After briefly working in advertising, a profession he grew to dislike intensely, Scarfe's early caricatures of public figures were published in satirical magazine Private Eye throughout the 1960s and 1970s. In the mid 1960s he took a job at the Daily Mail following a Dutch auction for his services with the Daily Express. His decision to work for the Daily Mail led to his estrangement from fellow cartoonist Ralph Steadman, alongside whom he had studied art at East Ham Technical College. Soon after, Steadman was commissioned to illustrate Scarfe and produced an image that was half saint and half Superman, but with a disconnected heart. Scarfe spent just a year working for the Daily Mail, during which time he was sent to provide illustrations from the Vietnam War.
Scarfe was approached to work with Pink Floyd after Roger Waters and Nick Mason both saw his animated BBC film A Long Drawn Out Trip. Pink Floyd's 1974 programme for their tour in the UK and US, in the form of a comic, included a centre-spread caricature of the band. Scarfe later produced a set of animated short clips used on the 1977 In The Flesh tour, including a full-length music video for the song Welcome to the Machine. He also drew the cover illustration for their 1979 album The Wall, and in 1982 worked on the film version of The Wall, although he and Waters fell out with director Alan Parker during the latter stages of editing. As well as the artwork, Scarfe contributed 15 minutes worth of elaborate animation to the film, including a sequence depicting the German bombing campaign over England during World War II, set to the song "Goodbye Blue Sky". He was also involved in the theatrical adaptation, including The Wall Concert in Berlin, where his animations were projected on a vast scale.
Scarfe continued to work with Roger Waters when he left Pink Floyd, creating the graphics and animation for Waters' solo album The Pros And Cons Of Hitch Hiking (1984) and its supporting tour.
Scarfe's collaboration with Waters was marked in 2008 by the release of a signed limited-edition eight-print series, "Scarfe On The Wall", which contained a monograph book with an extended new interview with Scarfe and was signed by Roger Waters.