He appeared in repertory in York and Birmingham 1943–45, and toured India and Burma in a production of Kenneth Horne's West End comedy Love in a Mist during 1945 with the Entertainments National Service Association (ENSA).

After appearances as Dr Bird in The Caine Mutiny Court Martial at the London Hippodrome in 1956, and Michael Claverton-Ferry in T. S. Eliot's The Elder Statesman, first at the Edinburgh Festival in 1958, then at the Cambridge Theatre, he joined the Old Vic Company for its 1959–60 season, among several parts taking the title role in Richard II, then stayed on for the 1960–61 season to play Mercutio in Romeo and Juliet, Oberon in A Midsummer Night's Dream and Malvolio in Twelfth Night.

William Rolfe in Hadrian the Seventh, winning his first Evening Standard Award as Best Actor for the London production and a Tony nomination after the transfer to Broadway.

In February 1973 he co-starred with Diana Rigg in Molière's The Misanthrope for which he won his second Evening Standard award; followed in July 1973 by the role of psychiatrist Martin Dysart ("played on a knife edge of professional skill and personal disgust by McCowen", according to Irving Wardle reviewing for The Times) in the world premiere of Peter Shaffer's Equus.

Christopher Hampton's stage adaptation of George Steiner's novel The Portage to San Cristobal of A.H. at the Mermaid in 1982 gave McCowen a great final speech, an attempted vindication of racial extermination delivered by Adolf Hitler, which for Guardian critic Michael Billington was "one of the greatest pieces of acting I have ever seen: a shuffling, grizzled, hunched, baggy figure, yet suggesting the monomaniac power of the Nuremberg Rallies, inhabiting the frail vessel of this old man's body."

While preparing to co-star as Vladimir to John Alderton's Estragon in Michael Rudman's acclaimed production of Waiting for Godot at the National Theatre in November 1987, McCowen also spent a busy autumn staging Martin Crimp's trilogy of short plays Definitely the Bahamas at the Orange Tree Theatre in Richmond upon Thames, having previously enjoyed Crimp's style of writing in a BBC radio version of Three Attempted Acts.

[5] McCowen appeared alongside Maureen Lipman and Arthur Askey performing comic monologues in The Green Tie on the Little Yellow Dog, which was recorded 1982, and broadcast by Channel 4 in 1983.

[citation needed] His later appearances included playing Albert Speer and Rudolf Hess in the BBC docudramas The World Walk in 1984 and 1985, and as astronomer Sir Frank Dyson in Longitude in 2000.

[citation needed] He was annoyed when no mention was made of his long-term male partner, fellow actor Geoffrey Burridge and threatened to stop the show from being broadcast.

McCowen was the narrator in a recording of Gerhard's cantata (after Camus) The Plague, with the Washington National Symphony Orchestra conducted by Antal Doráti in 1973, and also took the part of the Narrator in Stravinsky's Oedipus Rex, with Peter Pears, Kerstin Meyer and the London Philharmonic Orchestra conducted by Georg Solti; the music for this was recorded in March 1976, his spoken part later and the first issue was in February 1978.