In 1966, Doctor Who producer Innes Lloyd looked for a replacement for William Hartnell in the series' lead role. The continued survival of the show depended on audiences accepting another actor in the role, despite the bold decision that the replacement would not be a Hartnell lookalike or soundalike. Lloyd later stated that Hartnell had approved of the choice, saying, "There's only one man in England who can take over, and that's Patrick Troughton". Lloyd chose Troughton because of his extensive and versatile experience as a character actor. After he was cast, Troughton considered various ways to approach the role, to differentiate his portrayal from Hartnell's amiable-yet-tetchy patriarch. Troughton's early thoughts about how he might play the Doctor included a "tough sea captain", and a piratical figure in blackface and turban. Doctor Who creator Sydney Newman suggested that the Doctor could be a "cosmic hobo" in the mould of Charlie Chaplin, and this was the interpretation eventually chosen. Troughton was the first Doctor to have his face appear in the opening titles of the show. In one serial, The Enemy of the World, Troughton played two parts – as the protagonist (The Doctor) and the antagonist (Salamander).
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 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 (a full list of Doctor Who episodes missing from the BBC Archives is available here). Troughton found Doctor Who's schedule (at the time, 40 to 44 episodes per year) gruelling, 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 returned to Doctor Who three times after formally leaving the programme, 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, the 1972–73 serial opening the programme's 10th season. In 1983, 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 programme 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 programme's 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.