In 1957 Mulligan directed his first motion picture, Fear Strikes Out, starring Anthony Perkins as tormented baseball player Jimmy Piersall. The film was the first feature he would direct alongside longtime collaborator Alan J. Pakula, then a big-time Hollywood producer. Pakula once confessed that “working with Bob set me back in directing several years because I enjoyed working with him, and we were having a good time, and I enjoyed the work.”

Mulligan returned to television to direct episodes of Playhouse 90, Rendezvous, The Dupont Show of the Month, and TV versions of Ah, Wilderness! and The Moon and Sixpence. In 1959 he won an Emmy Award for directing The Moon and Sixpence, a television production that was the American small-screen debut of Laurence Olivier.

Mulligan began the 1970s with The Pursuit of Happiness (1971), based on the 1968 novel by Thomas Rogers, which had been a finalist for the National Book Award. The film starred Michael Sarrazin as William Popper, a college student (disillusioned with both right-wing and left-wing American politics) whose life is complicated when he accidentally runs over and kills an elderly woman and is quickly sentenced to one year in prison for vehicular manslaughter. He then contemplates breaking out of prison and fleeing the country with his girlfriend (played by Barbara Hershey), since neither feels their lives have made any significant difference in America.

Also in 1971, Mulligan released Summer of ’42 (1971), which was based on the coming-of-age novel by Herman Raucher and starred Gary Grimes as a teenage stand-in for Raucher who spends a summer vacation in 1942 on Nantucket Island lusting after a young woman (Jennifer O’Neill) whose husband has shipped off to fight in the war. A box office smash, Summer of ’42 went on to gross over $20 million, and Mulligan was nominated for a Golden Globe Award for Best Director.

Mulligan described his role as a director thusly: “Things have to sift through me. That’s me up there on the screen. The shooting, the editing, the use of music—all that represents my attitude toward the material.” In a 1978 interview with the Village Voice, he insisted, “I don’t know anything about ‘the Mulligan style.’ If you can find it, well, that’s your job.”

Mulligan also had his critics. Actor James Caan described him as the most incompetent filmmaker he had ever worked with saying “A lot of mediocrity was produced” following their work on Kiss Me Goodbye in 1982. Caan cited his experiences as a key reason why he made no movies for 5 years from 1982 to 1987.

Later in March 1992, Mulligan made headlines when he angrily took his name off of airline cuts of The Man in the Moon, after he had learned that the film would be heavily censored by American and Delta flights. In an interview with Ebert, Mulligan explained, “The airlines demanded so many excessive and unreasonable cuts and changes that I took my name off the film… it’s the first time I’ve ever done that.”

Before his death in 2008, Mulligan had commissioned playwright Beth Henley to write a screenplay from the novel A Long and Happy Life by Reynolds Price, which Mulligan had bought the rights to with his own money. The film was never made.

Mulligan died of heart disease at his home in Lyme, Connecticut on December 20, 2008, at the age of 83.