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1961–1971: Established actor

In 1961, Brando made his directorial debut in the western One-Eyed Jacks. The picture was originally directed by Stanley Kubrick, but he was fired early in the production. Paramount then made Brando the director. Brando portrays the lead character Rio, and Karl Malden plays his partner "Dad" Longworth. The supporting cast features Katy Jurado, Ben Johnson, and Slim Pickens. Brando's penchant for multiple retakes and character exploration as an actor carried over into his directing, however, and the film soon went over budget; Paramount expected the film to take three months to complete but shooting stretched to six and the cost doubled to more than six million dollars. Brando's inexperience as an editor also delayed postproduction and Paramount eventually took control of the film. Brando later wrote, "Paramount said it didn't like my version of the story; I'd had everyone lie except Karl Malden. The studio cut the movie to pieces and made him a liar, too. By then, I was bored with the whole project and walked away from it". One-Eyed Jacks was received with mixed reviews by critics.

Brando's revulsion with the film industry reportedly boiled over on the set of his next film, Metro-Goldwyn-Mayer 's remake of Mutiny on the Bounty, which was filmed in Tahiti. The actor was accused of deliberately sabotaging nearly every aspect of the production. On June 16, 1962, The Saturday Evening Post ran an article by Bill Davidson with the headline "Six million dollars down the drain: the mutiny of Marlon Brando". Mutiny director Lewis Milestone claimed that the executives "deserve what they get when they give a ham actor, a petulant child, complete control over an expensive picture." Mutiny on the Bounty nearly capsized MGM and, while the project had indeed been hampered with delays other than Brando's behavior, the accusations would dog the actor for years as studios began to fear Brando's difficult reputation. Critics also began taking note of his fluctuating weight.

Distracted by his personal life and becoming disillusioned with his career, Brando began to view acting as a means to a financial end. Critics protested when he started accepting roles in films many perceived as being beneath his talent, or criticized him for failing to live up to the better roles. Previously only signing short-term deals with film studios, in 1961 Brando uncharacteristically signed a five-picture deal with Universal Studios that would haunt him for the rest of the decade. The Ugly American (1963) was the first of these films. Based on the 1958 novel of the same title that Pennebaker had optioned, the film, which featured Brando's sister Jocelyn, was rated fairly positively but died at the box office. Brando was nominated for a Golden Globe for his performance. All of Brando's other Universal films during this period, including Bedtime Story (1964), The Appaloosa (1966), A Countess from Hong Kong (1967) and The Night of the Following Day (1969), were also critical and commercial flops. Countess in particular was a disappointment for Brando, who had looked forward to working with one of his heroes, director Charlie Chaplin. The experience turned out to be an unhappy one; Brando was horrified at Chaplin's didactic style of direction and his authoritarian approach. Brando had also appeared in the spy thriller Morituri in 1965; that, too, failed to attract an audience.

Brando acknowledged his professional decline, writing later, "Some of the films I made during the sixties were successful; some weren't. Some, like The Night of the Following Day, I made only for the money; others, like Candy, I did because a friend asked me to and I didn't want to turn him down... In some ways I think of my middle age as the Fuck You Years." Candy was especially appalling for many; a 1968 sex farce film directed by Christian Marquand and based on the 1958 novel by Terry Southern, the film satirizes pornographic stories through the adventures of its naive heroine, Candy, played by Ewa Aulin. It is generally regarded as the nadir of Brando's career. The Washington Post observed: "Brando's self-indulgence over a dozen years is costing him and his public his talents." In the March 1966 issue of The Atlantic, Pauline Kael wrote that in his rebellious days, Brando "was antisocial because he knew society was crap; he was a hero to youth because he was strong enough not to take the crap", but now Brando and others like him had become "buffoons, shamelessly, pathetically mocking their public reputations." In an earlier review of The Appaloosa in 1966, Kael wrote that the actor was "trapped in another dog of a movie... Not for the first time, Mr. Brando gives us a heavy-lidded, adenoidally openmouthed caricature of the inarticulate, stalwart loner." Although he feigned indifference, Brando was hurt by the critical mauling, admitting in the 2015 film Listen to Me Marlon, "They can hit you every day and you have no way of fighting back. I was very convincing in my pose of indifference, but I was very sensitive and it hurt a lot."

Brando portrayed a repressed gay army officer in Reflections in a Golden Eye, directed by John Huston and co-starring Elizabeth Taylor. The role turned out as one of his most acclaimed in years, with Stanley Crouch marveling, "Brando's main achievement was to portray the taciturn but stoic gloom of those pulverized by circumstances." The film overall received mixed reviews. Another notable film was The Chase (1966), which paired the actor with director Arthur Penn, Jane Fonda, Robert Redford and Robert Duvall. The film deals with themes of racism, sexual revolution, small-town corruption, and vigilantism. The film was received mostly positively.

Brando cited Burn! (1969) as his personal favorite of the films he had made, writing in his autobiography: "I think I did some of the best acting I've ever done in that picture, but few people came to see it." Brando dedicated a full chapter to the film in his memoir, stating that the director, Gillo Pontecorvo, was the best director he had ever worked with next to Kazan and Bernardo Bertolucci. Brando also detailed his clashes with Pontecorvo on the set and how "we nearly killed each other." Loosely based on events in the history of Guadeloupe, the film got a hostile reception from critics. In 1971, Michael Winner directed him in the British horror film The Nightcomers with Stephanie Beacham, Thora Hird, Harry Andrews and Anna Palk. It is a prequel to The Turn of the Screw, which had previously been filmed as The Innocents (1961). Brando's performance earned him a nomination for a Best Actor BAFTA, but the film bombed at the box office.