During his time on the series, Troughton tended to shun publicity and rarely gave interviews. He told one interviewer, "I think acting is magic. If I tell you all about myself it will spoil it". Years later, he told another interviewer that his greatest concern was that too much publicity would limit his opportunities as a character actor after he left the role.
A rare interview with Ernest Thompson from Radio Times reveals that Troughton "always liked dressing up, and would have been happy as a school teacher as children keep one young". Troughton gave away the secret of what Jamie (Frazer Hines) wore underneath his kilt – "khaki shorts". Troughton was popular with both the production team and his co-stars. Producer Lloyd credited Troughton with a "leading actor's temperament. He was a father figure to the whole company and hence could embrace it and sweep it along with him". Troughton also gained a reputation on set as a practical joker.
Many of the early episodes in which Troughton appeared were among those discarded by the BBC. Troughton found Doctor Who's schedule (at the time, 40 to 44 episodes per year) grueling, and decided to leave the series in 1969, after three years in the role. This decision was also motivated in part by fear of being typecast. Troughton's decision would eventually become something of an unwritten law (the "Troughton Rule") among actors, to prevent one from becoming typecast in a particular role in a potentially long-running television program.
Troughton returned to Doctor Who three times after formally leaving the program, returning to the character more than any other actor who portrayed the Doctor after ending his regular connection with the series. The first of these occasions was in The Three Doctors, a 1973 serial celebrating the program's 10th anniversary. Ten years later, Troughton overcame some reluctance to reprise his role and agreed to appear in the 20th anniversary special The Five Doctors at the request of series producer John Nathan-Turner. He also agreed to attend Doctor Who conventions including the show's 20th anniversary celebrations at Longleat in 1983. He also appeared around the world with Nathan-Turner. Troughton enjoyed the return to the program so much that he readily agreed to appear one more time as the Second Doctor, with Colin Baker's Sixth Doctor in The Two Doctors (1985). Reportedly, he also advised the Fifth Doctor, actor Peter Davison, to limit his time in the role to three seasons to avoid typecasting and the younger actor followed this advice.
In 2013, the BBC commissioned a docudrama about the early days of Doctor Who, as part of the program fiftieth anniversary celebrations. Troughton appears as a character in the production, called An Adventure in Space and Time, portrayed by actor Reece Shearsmith.
In 2014's "Robot of Sherwood", a still image of Troughton from 1953 appears among the future depictions of Robin Hood displayed by the Twelfth Doctor to the outlaw.