Miike was born in Yao, Osaka, Japan, an area inhabited by the working class and immigrants, mostly from Korea. His family was originally from Kumamoto Prefecture. During World War II, his grandfather was stationed in China and Korea, and his father was born in Seoul. His father worked as a welder and his mother as seamstress. Although he claimed to have attended classes only rarely, he graduated from Yokohama Vocational School of Broadcast and Film (Yokohama Hoso Eiga Senmon Gakko) under the guidance of renowned filmmaker Shohei Imamura, the founder and Dean of that institution.

Miike's first films were television productions, but he also began directing several direct-to-video V-Cinema releases. Miike still directs V-Cinema productions intermittently due to the creative freedom afforded by the less stringent censorship of the medium and the riskier content that the producers will allow.

Miike's theatrical debut was the film The Third Gangster (Daisan no gokudô). However it was Shinjuku Triad Society (1995) that was the first of his theatrical releases to gain public attention. The film showcased his extreme style and his recurring themes, and its success gave him the freedom to work on higher-budgeted pictures. Shinjuku Triad Society is also the first film in what is labeled his "Black Society Trilogy", which also includes Rainy Dog (1997) and Ley Lines (1999). He gained international fame in 2000 when his romantic horror film Audition (1999) and his violent yakuza epic Dead or Alive (1999) played at international film festivals. He has since gained a strong cult following in the West that is growing with the increase in DVD releases of his works.

Miike has garnered international notoriety for depicting shocking scenes of extreme violence and sexual perversions. Many of his films contain graphic and lurid bloodshed, often portrayed in an over-the-top, cartoonish manner. Much of his work depicts the activities of criminals (especially yakuza) or concern themselves with non-Japanese living in Japan. He is known for his black sense of humor and for pushing the boundaries of censorship as far as they will go.

Despite his notorious reputation, Miike has also proven himself to be capable of directing lighthearted children's films (Zebraman, The Great Yokai War), touching period pieces (Sabu), and subdued, moving pictures such as the road movie The Bird People in China. Even in his more violent work, he is given to moments of surprising sentimentality, as in Dead or Alive 2: Birds. His dabbling in every sort of genre and emotional range is a testament to his versatility as a director, though a lot of his output is genre-defying. For example, The Happiness of the Katakuris is an unconventional farcical musical-comedy-horror involving bizarre claymation sequences, zombies and b-movie pastiches.

Other less controversial works include Ley Lines and Agitator, which are character-driven, serious crime dramas. Graveyard of Honor (2002) is a remake of the 1975 Kinji Fukasaku film by the same name. Andoromedeia, perhaps one of his less renowned films, is a teen drama starring the J-pop girl-group Speed.

Critics have sometimes noted the puzzling discrepancy of Miike's artistic development noting that he appears to be simultaneously becoming more radical and more mainstream a director. Films like One Missed Call and The Great Yokai War are his most commercial works to date while films like Izo and the "Box" segment in Three... Extremes are less accessible and target arthouse audiences and fans of extreme cinema.

Despite Miike's voluminous output, it would be erroneous to consider him a dilettante or a director for hire. Academics have recognized Miike as an auteur, noting much depth as well as stylistic and thematic consistency in his body of work. Recurring themes and imagery in his work include reincarnation, birds, family, alienation, chaos and order. Films like Visitor Q and Izo are highly philosophical beneath their violent, taboo-laden exterior. This mingled with his imaginative and often idiosyncratic cinematography makes his work instantly recognizable regardless of the genre he works in.

One of his most controversial films was the ultra-violent Ichi the Killer (2001), adapted from a manga of the same name and starring Tadanobu Asano as a sadomasochistic yakuza enforcer. The extreme violence was initially exploited to promote the film: during its international premiere at the Toronto International Film Festival in 2001, the audience received "barf bags" emblazoned with the film's logo as a promotional gimmick (one typically flamboyant gory killing involves a character slicing a man in half from head to groin, and severing another's face, which then slides down a nearby wall).

However, the British Board of Film Classification refused to allow the release of the film uncut in Britain, citing its extreme levels of sexual violence towards women (despite the fact that there are possibly equal amounts of sexual violence towards men). In Hong Kong, 15 minutes of footage were cut. In the United States it has been shown uncut (unrated). An uncut DVD was also released in the Benelux.