Singleton was born in Los Angeles, the son of Sheila Ward-Johnson, a pharmaceutical company sales executive, and Danny Singleton, a real estate agent, mortgage broker, and financial planner. He attended Pasadena City College and the USC School of Cinematic Arts. He graduated from USC in 1990, and is a member of Kappa Alpha Psi fraternity. Singleton was enrolled in the University of Southern California's Filmic Writing program under Margaret Mehring and her now famous curriculum. The program was designed to take students directly into the Hollywood system as proficient writer/directors.
Unlike the other standard USC programs for screenwriting, film production, or the Peter Stark Motion Picture Producing and critical studies programs, Mehring designed her FILMIC writing program to teach a select group of students how to be authors of their visions. Other students included Helen Childress (writer of Reality Bites), Stephen Chbosky (writer of TV’s Jericho), and Ms. Childress’ husband Carlos Brooks (writer/director of Quid Pro Quo). Singleton was always present in the Apple computer writing lab, working on his screenplays during late nights and early mornings. However, his ability to direct was correlated to an early beginning in music videos, which culminated in the EFX driven Michael Jackson “Remember the Time” MTV video.
On October 12, 1996, John married Ghanaian actress Akosua Gyamama Busia, an actress and the daughter of Ghana's second Prime Minister Dr. Kofi Abrefa Busia. They have a daughter named Hadar Singleton who was born on April 3, 1997, who has appeared in Tears of the Sun (2003) and other productions. John also has a daughter named Justice Maya Singleton (born on October 17, 1992) with ex-companion Tosha Lewis, as well as a son, Maasai Mohandas Singleton (born April 3, 1994). He has six children in total.
On August 23, 2007, Singleton was involved in an automobile accident in which he struck a jaywalking pedestrian, Constance Russell, 57, of Los Angeles. Staying on the scene until police arrived, Singleton was not under the influence of alcohol or other substances, and was released after being questioned. Russell died later in the hospital. The case was turned over to the District Attorney but no charges were filed.