Baker was born in Fountains Road, Bootle, Merseyside. His father, John Stewart Baker, was a sailor who was rarely at home, resulting in Tom being raised largely by his mother Mary Jane in her Roman Catholic faith. He left school at 15 to become a novice monk and remained in the monastic life for six years, but left and went into the Merchant Navy, at the same time taking up acting, at first as a hobby. In 1972,he got his first big break with the role of Rasputin in the film Nicholas and Alexandra (which also starred Michale Jayston, who later played the Valeyard). Other early roles for Baker included Lynch in The Mutations, Jenkin in "The Miller's Tale" segment of The Canterbury Tales, and Dr. Ahmed el Kabir in a BBC telelvision version of The Millionairess, co-starring Maggie Smith.
In 1974, Baker took on the role of the Doctor from Jon Pertwee. He was cast largely because of his performance as the evil sorcerer Koura in The Golden Voyage of Sinbad.
Baker was working as a brick hauler on a construction site at the time, as acting jobs were scarce. Initially he was dubbed "Boiler Suit Tom" by the media, as he had been supplied with some old studio set clothes to replace his modest garments at a press conference.
He quickly made the part his own. As the Doctor, his eccentric style of dress and speech — particularly his trademark long scarf and fondness for jelly babies — made him an immediately recognisable figure, and he quickly caught the viewing public's imagination. His decision to move on in 1981 was regretted by many of the programme's fans, and his incarnation is generally regarded as the most popular of the Doctors (his nearest rival not arriving unti David Tennant in the 2000s). Baker played the Doctor for seven consecutive seasons over a seven-year period, making him the longest-serving actor in the part.