Imamura was born to a comfortably upper-middle-class doctor's family in Tokyo in 1926. For a short time after 1945, when Japan was in a devastated condition following the war, Imamura participated in the black market selling cigarettes and liquor. Reflecting this period of his life, Imamura's interests as a filmmaker were usually focused on the lower strata of Japanese society. He studied Western history at Waseda University, but spent more time participating in theatrical and political activities. He cited a viewing of Akira Kurosawa's Rashomon in 1950 as an early inspiration, and said he saw it as an indication of the new freedom of expression possible in Japan in the post-war era.

Upon graduation from Waseda in 1951, Imamura began his film career working as an assistant to Yasujirō Ozu at Shochiku Studios on the films Early Summer (1951), The Flavor of Green Tea over Rice (1952) and Tokyo Story (1953). Imamura, however, was uncomfortable with the way Ozu portrayed Japanese society. While Imamura's films were to have a quite different style from Ozu's, Imamura, like Ozu, was to focus on what he saw as particularly Japanese elements of society in his films. "I've always wanted to ask questions about the Japanese, because it's the only people I'm qualified to describe," he said. He expressed surprise that his films were appreciated overseas.

Imamura left Shochiku in 1954 for a better salary at Nikkatsu. There he worked as an assistant Director to Yuzo Kawashima and also co-authored the screenplay to Kawashima's Sun in the Last Days of the Shogunate. Much later he edited a book about Kawashima, entitled Sayonara dake ga jinsei da.

In 1958, at Nikkatsu, Imamura made his first film, Stolen Desire. With this early tale of traveling actors, Imamura indulged in some of the controversial and eccentric themes that were to mark his career as a filmmaker. Nikkatsu, however, was not enthusiastic about his more radical tendencies, and forced him to make a series of lighter films with which he was not happy. Nishi Ginza Station was a comedy based on a pop-song. Endless Desire and My Second Brother were similar light fare that did not satisfy Imamura.

His 1961 film, Pigs and Battleships was a wild and energetic story about the U.S. military base at Yokosuka and its relationship with lower elements of Japanese society. Shocked by the film and what they perceived as anti-American sentiments, Nikkatsu did not allow Imamura another project for two years. His next films, 1963's The Insect Woman and 1964's Unholy Desire showed no toning down of his style. With these three films, Imamura had established himself as a Director with a strong and unique vision, and one of the leading figures of the Japanese New Wave.

To more freely explore themes without studio interference, he established his own production company, Imamura Productions, in 1965. His first independent feature was a free adaptation of Akiyuki Nosaka's 1963 novel about life on the fringes of Osaka society, The Pornographers.

He next made his first venture into the documentary genre with 1967's A Man Vanishes. His 1968 film The Profound Desire of the Gods investigates the clash between modern and traditional societies on a southern Japanese island. One of Imamura's more ambitious and costly projects, this film's poor box-office performance led to a retreat back into smaller, documentary-like films for the next decade.

History of Postwar Japan as Told by a Bar Hostess and Karayuki-san, the Making of a Prostitute were two of these projects, both focusing on one of his favorite themes: Strong women who survive on the periphery of Japanese society. Imamura returned to fiction with 1979's Vengeance Is Mine, though this film about a serial killer is based on a true story.

His eldest son Daisuke Tengan is also a script Writer and film Director, and worked on the screenplays to Imamura's films The Eel (1997), Dr. Akagi (1998), Warm Water Under a Red Bridge (2001) and 11'09"01 September 11 (2002).

Imamura played the role of a Historian in the 2002 South Korean film 2009 Lost Memories.