Kinji Fukasaku was born in 1930 in Mito, Ibaraki Prefecture as the youngest of five children. When he was 15 years old, Fukasaku's class was drafted, and he worked as a munitions worker during World War II. In July 1945, the class was caught in bombing. Since the children could not escape the bombs, they had to dive under each other in order to survive. The surviving members of the class had to dispose of the corpses. After the war, he spent much of his time watching foreign films.

Fukasaku studied cinema at Nihon University, in the country's first film department, before switching to the literature department for scriptwriting his junior year. There he studied under Kogo Noda and Katsuhito Inomata. After graduating in 1953, Fukasaku became an assistant Director at Toei in June 1954, where he worked under people such as Masahiro Makino and Yasushi Sasaki.

Fukasaku made his directorial debut in 1961 with the two featurettes Wandering Detective: Tragedy in Red Valley and Wandering Detective: Black Wind in the Harbor, starring Sonny Chiba. His first feature length, for the New Toei subsidiary was High Noon for Gangsters that same year. His first film for the Toei Company proper was The Proud Challenge the following year starring Kōji Tsuruta. He had his breakthrough hit in 1964 with Ken Takakura starring in Jakoman and Tetsu. From 1966 to 1971, he created several modern gang films for Toei usually starring Tsuruta, such as Kaisanshiki (1967), Bakuto Kaisanshiki (1968) and Nihon Boryokudan: Kumicho (1969).

Thanks to a non-exclusive contract, he also directed Black Lizard, based on Yukio Mishima's stage adaptation of the Edogawa Rampo novel, and Black Rose Mansion for Shochiku both of which starred the transvestite actor Akihiro Miwa. In 1968 he directed The Green Slime, a United States-Japan science fiction co-production.

In 1970, Fukasaku was recruited to direct the Japanese portion of another US-Japan film, Tora! Tora! Tora!, after Akira Kurosawa pulled out. Using his pay from the project, he bought the rights to adapt Under the Flag of the Rising Sun. The movie was critically acclaimed, even being selected as Japan's entry for Best Foreign Language Film at the 45th Academy Awards in 1972, although it was not accepted as a nominee. That year also saw the release of Street Mobster starring Bunta Sugawara, which resulted in Toei Producer Koji Shundo selecting Fukasaku to direct a groundbreaking yakuza film. Battles Without Honor and Humanity was released in 1973. Up to this point, Japan's many yakuza films had usually been tales of chivalry set in the pre-war period, but Fukasaku's ultra-violent, documentary-style film took place in chaotic post-War Hiroshima. A commercial and critical success, it gave rise to seven sequels by Fukasaku and three movies that are based on the series but directed by others. After directing several more yakuza films, Graveyard of Honor (1975), Cops vs. Thugs (1975), Yakuza Graveyard (1976), and Hokuriku Proxy War (1977), Fukasaku left the genre.

He focused on historical epics; Shogun's Samurai (1978), The Fall of Ako Castle (1978), Samurai Reincarnation (1981); and science fiction; Message from Space (1978) and Virus (1980). Virus was Japan's most expensive production at the time, and became a financial flop. However, two years after it he directed the highly acclaimed comedy Fall Guy, winning both the Japan Academy Prize for Picture of the Year and Kinema Junpo Award for Best Film of the Year. Fukasaku was chosen to direct 1989's Violent Cop, but a scheduling conflict caused him to pull out and Takeshi Kitano took over in his first directorial role.

In 1997, he received the Purple Medal of Honor from the Japanese government for his work in film.

Near the end of his life, Fukasaku branched out into the world of video games by serving as the Director of the Capcom/Sunsoft survival horror game Clock Tower 3. In 2000, Battle Royale was released. The highly controversial film received positive critical praise and became a major financial success, grossing ¥3.11 billion domestically.

Fukasaku announced he had prostate cancer in September 2002. In late December 2002, shortly after filming began on Battle Royale II: Requiem, he was hospitalized when his condition worsened. Fukasaku died at a Tokyo hospital on January 12, 2003, aged 72. Having directed only a single scene, his son, Kenta took over the film.