His work on Doctor Who began in 1975 when he provided some accompanying incidental music for Revenge of the Cybermen and special sound for Planet of Evil. When John Nathan-Turner became producer of Doctor Who in 1980, he decided that the music needed to be updated and commissioned Howell to provide a new arrangement of the Doctor Who theme to accompany a new title sequence. Whereas the original arrangement of the theme (written by Ron Grainer) had been realised by Delia Derbyshire using musique concrète techniques, Howell arranged Grainer's theme on analogue synthesisers - primarily using a Yamaha CS-80 and an ARP Odyssey Mk3.
Howell's new arrangement first appeared in 1980 on The Leisure Hive, for which Howell had also recorded the incidental score, and was used throughout Tom Baker's final season on the programme as well as Peter Davison's tenure as the Doctor. For Colin Baker's first season in 1984, however there was a problem in transferring the music so the theme was slightly lower in pitch. This version continued to be used until Colin Baker's 1985 story, Revelation of the Daleks. Between 1980 and 1985 Howell also provided incidental music for ten stories of Doctor Who. In 1986, Nathan-Turner commissioned a new theme arrangement by Dominic Glynn which ended Howell's association with Doctor Who on television, although he did provide music for the radio series The Paradise of Death and The Ghosts of N-Space as well as a new version of his theme for use in the Big Finish audio dramas.