Satoshi Kon was born on October 12, 1963, and he comes from Kushiro, Hokkaido, Japan. Kon attended Musashino College of the Arts, with the intention of becoming a painter. However, after college, he ended up working with Katsuhiro Otomo on a manga titled World Apartment Horror, which was published in Young Magazine. Kon would also serve as an editor at Young Magazine before moving into anime.

Kon got his start in the anime industry in 1991, when he worked as a set designer for the anime film, Roujin Z; Otomo also worked on this series as a screenwriter and mechanical designer. Kon made his anime screenwriting debut in 1995 when he wrote the "Magnetic Rose" section of Memories, an anthology film directed by Katsuhiro Otomo. It has been said that Kon's early work in anime was strongly influenced by Otomo, due to how much the two of them worked together during Kon's early years in the manga and anime industries.

In 1997, Kon made his anime directorial debut with Perfect Blue. The production was originally intended to be an original video animation, but it was turned into a feature film in the middle of production. After Perfect Blue, Kon went on to direct Millennium Actress, Tokyo Godfathers, Paprika, the television series Paranoia Agent, and "Good Morning" (which is part of Ani*Kuri15, a series of 15 one-minute shorts that aired on the Japanese TV station NHK between 2007 and 2008). All of Kon's work as an anime director was made by Studio Madhouse, where he served as a staff director, alongside Rintaro and Yoshiaki Kawajiri. Kon's work has a strong emphasis on the psychological well-being of his characters. In Tokyo Gofathers, he explored themes of personal guilt, loss, and suicidal ideation. In films such as Paprika and Millennium Actress, Kon steps between the boundaries of fantasy and reality (such as breaking the fourth wall), and he has characters performing actions that are impossible in the real world.

In addition to writing "Magnetic Rose" for Memories, Kon also wrote the screenplays for the films Millennium Actress, Tokyo Godfathers, and Paprika. Kon also contributed as an animator on the films Perfect Blue, Millennium Actress, and Tokyo Godfathers. Kon was also a founder and part of the 15-member steering committee of the Japan Animation Creators Association (JAniCA) labor group.

Sadly, Satoshi Kon passed away on August 23, 2010 at the age of 46. After his death, statements posted by Kyoko Kon (Satoshi Kon's wife) and the Madhouse studio, said that the cause of his death was pancreatic cancer.