Clarke played bass guitar in skiffle bands in the middle and late 1950s, and continued playing in rock bands into the early 1960s. Alongside this, he found work as a session musician for Decca Records, and in 1963 he was hired by the label as a promoter. In 1964 he transferred to the production department, working under Dick Rowe.
Most of his early work was spent on clerical and discographical tasks, though he also worked as a songwriter; his tune "Our Song" was recorded by Malcolm Roberts (who had a hit with it in South America) and Jack Jones. He produced his first single with Pinkerton's Assorted Colours; that song, "Mirror, Mirror", became a #8 hit on the UK Singles Chart. He also produced The Equals's #1 hit "Baby Come Back" and wrote "The Guy Who Made Her A Star" for the band, featured on the b-side of the band's 1968 hit single, "Laurel And Hardy".
He was assigned to work with the Moody Blues starting in 1966, when the group was fading after its first major hit, "Go Now". He worked with them on the single "Fly Me High", and following this was put in charge of a project to create a rock version, with the Moody Blues, of Antonin Dvorak's New World Symphony. After this idea was shelved, he produced what became their 1967 symphonic rock album Days of Future Passed. Like the members of the Moody Blues themselves, Clarke had received no formal training in classical music as a youngster. He worked with them closely over the course of their next six albums, helping them develop a complex sound which, among other things, involved copious use of the mellotron (and earning the nickname "the Sixth Moody" from fans). When the Moody Blues set up their own label, Threshold Records, Clarke attempted to have them sign King Crimson, though the deal never came to fruition.
Aside from the Moody Blues, Clarke also worked with Providence and on the album Blue Jays, by Moody Blues members Justin Hayward and John Lodge. He produced The Four Tops for a UK only release in 1972, which was comprised entirely of songs written by the Moody Blues.
After the Moody Blues went on hiatus in the middle of the 1970s, he worked to have them reunite, and produced their 1978 comeback album, Octave; however, he elected not to continue working with them after this album. Subsequently he produced for Clannad, Rick Wakeman, and Nicky Hopkins, among others.