After receiving a fellowship with the PIA, Sono made his first feature-length 16 mm film in 1990, Bicycle Sighs (Jitensha Toiki), a coming-of-age tale about two underachievers in the perfectionist Japan. Sono co-wrote, directed, and starred in the film.
In 2005 he wrote and directed Into a Dream (Yume no Naka e), which also released as a novel later on, and was a coming-of-age tale much in the style of his first film Bicycle Sighs, about the life of a theatre group member and his quest to find who he is. Few weeks after that, he released the Suicide Circle's second part, based on the Kanzenban novel. Noriko's Dinner Table was also directed and written by him, and was part of twelve film festivals worldwide. For this movie he worked with many first-time actors, and took the Suicide Circle story into a different level. For his efforts, he received a Don Quijote Award and a Special Mention at the Karlovy Vary Film Festival.
At the end of 2005, Sion Sono also premiered a personal project with actors Issei Ishida and Masumi Miyazaki. Strange Circus (Kimyô na Sâkasu), directed, written, composed and cinematographed by Sono, took elements from the Grand Guignol theater and a story from the minds of both Masumi and Sono, filled with incest, sexual abuse, terrible family issues, extreme gore, and a twisted sense of reality.
In 2008, he was the director and writer of Love Exposure. Love Exposure is the first film in Sono's "Hate" trilogy; the films Cold Fish, released in 2010, and Guilty of Romance, released in 2011, are the second and third installments of the trilogy respectively. In 2013 he directed the Action-Drama Why Don't You Play in Hell? (Jigoku de naze warui). Following shortly after, he directed an adaptation of popular manga series Tokyo Tribe.