Despite being catapulted to fame by the aforementioned films, Courtenay has said that he has not particularly enjoyed film acting; and from the mid-1960s concentrated more on stage work. In 1968 Courtenay began a long association with Manchester when he played in The Playboy of the Western World for the Century Theatre at Manchester University directed by Michael Elliott. In 1969 Courtenay played Hamlet (John Nettles playing Laertes) for 69 Theatre Company at University Theatre in Manchester, this being the precursor of the Royal Exchange Theatre, which was founded in 1976 where he was to give many performances, firstly under the direction of Casper Wrede. His first roles for the Royal Exchange were as Faulkland in Richard Brinsley Sheridan's The Rivals and the hero of Heinrich von Kleist's The Prince of Homburg. Since then he has played a variety of roles, including in 1999 the leading role in the theatre's production of King Lear, and in 2001 Uncle Vanya.
Courtenay's film debut was in 1962 with Private Potter, directed by Finnish-born Director Caspar Wrede, who had first spotted Courtenay while he was still at RADA. This was followed by The Loneliness of the Long Distance Runner, directed by Tony Richardson and Billy Liar, two highly acclaimed films and performances which helped usher in the British New Wave of the early-to-mid-1960s. For these performances Courtenay was awarded the 1962 BAFTA Award for most promising newcomer and the 1963 BAFTA Award for best actor respectively. He also was the first to record the song Mrs. Brown, You've Got a Lovely Daughter, doing so for the TV play The Lads. The song was released by Decca on a 45 rpm record.
For his role as the dedicated revolutionary leader Pasha Antipov in Doctor Zhivago (1965), he was nominated for an Academy Award for Best Supporting Actor, but was bested by Martin Balsam. Among his other well-known films is King & Country, directed by Joseph Losey, where he played opposite Dirk Bogarde; the all-star war film, Operation Crossbow, directed by Michael Anderson (starring George Peppard and Sophia Loren); King Rat, directed by Bryan Forbes and costarring James Fox and George Segal; and The Night of the Generals, directed by Anatole Litvak with Peter O'Toole and Omar Sharif.
Courtenay's working relationship with Wrede returned to film when he played the title role in the latter's 1970 production of One Day in the Life of Ivan Denisovich. His best known film role since then was in The Dresser, from Ronald Harwood's play of the same name (in which he also appeared) with Albert Finney. Both Courtenay and Finney received nominations for Best Actor in the 1984 Academy Awards for their roles, losing to Robert Duvall. He played the father of Derek Bentley (Christopher Eccleston) in the 1991 film Let Him Have It.
Courtenay's television and radio appearances have been relatively few, but have included She Stoops to Conquer in 1971 on BBC and several Ayckbourn plays. He appeared in I Heard the Owl Call My Name on US television in 1973. In 1994 he starred as Quilp opposite Peter Ustinov in a Disney Channel 'made for television' version of The Old Curiosity Shop. Rather unexpectedly, he had a cameo role as the Anthropologist Bronisław Malinowski in the 1995 US TV film Young Indiana Jones and the Treasure of the Peacock's Eye. In 1998 he teamed with Albert Finney again for the acclaimed BBC drama A Rather English Marriage. He played the role of God, opposite Sebastian Graham-Jones, in Ben Steiner's radio play "A Brief Interruption", broadcast on BBC Radio 4 in 2004. In the same year, he played the role of Stanley Laurel in Neil Brand's radio play 'Stan', broadcast on Radio 4. Also for Radio 4, he played the title role in Nick Leather's The Domino Man of Lancashire and Maurice in Richard Lumsden's Man in the Moon, both broadcast in 2007. Courtenay also appeared in the 2008 Christmas special of the BBC show The Royle Family, playing the role of Dave's father, David Sr.
In 1999, Courtenay was awarded an honorary doctorate by Hull University.
In 2000, Courtenay's memoir Dear Tom: Letters From Home was published to critical acclaim. It comprises a selection of the letters exchanged between Courtenay and his mother, interspersed with his own recollections of life as a young student actor in London in the early 1960s.
In 2002, based on an idea by Michael Godley, Courtenay compiled a one-man show Pretending To Be Me based on the letters and writings of poet Philip Larkin, which first played at the West Yorkshire Playhouse in Leeds. It later transferred to the Comedy Theatre in the West End in London.
In 2007, Courtenay appeared in two films: Flood, a disaster epic in which London is overwhelmed by floods, and The Golden Compass, an adaptation of Philip Pullman's novel, playing the part of Farder Coram. In 2008, he appeared in the BBC adaptation of Little Dorrit by Charles Dickens, playing william Dorrit, and the Christmas edition of The Royle Family, playing David (Senior). In March 2011, he joined the cast of Gambit, a film starring fellow RADA alumnus Alan Rickman that began filming in May. The film was released in Great Britain in November 2012. In 2012, he co-starred in Quartet, directed by Dustin Hoffman.
On 19 January 2018 Sir Tom was bestowed the Honorary Freedom of the City of Hull.
