Sonnenfeld was born and raised in New York City, the son of Irene "Kelly" (Kellerman), an art Teacher, and Sonny Sonnenfeld, a lighting salesman, educator, and architectural lighting designer. He was raised in a Jewish family. After he received his bachelor's degree from Hampshire College, he graduated from New York University of Film School in 1978.

He began working on pornographic films, before starting work as Director of photography on the Oscar-nominated In Our Water (1982). Then Joel Coen and Ethan Coen hired him for Blood Simple (1984). This film began his collaboration with the Coen brothers, who used him for their next two pictures, Raising Arizona (1987) and Miller's Crossing (1990). He also worked with Danny DeVito on Throw Momma from the Train (1987) and Rob Reiner on When Harry Met Sally (1989) and Misery (1990).

Sonnenfeld gained his first work as a Director from Paramount Pictures on The Addams Family, a box-office success released in November 1991. Its sequel, Addams Family Values (1993), was not as successful at the box office, but he received critical acclaim for his fourth directorial outing, Get Shorty (1995). Produced by Jersey Films and based on a novel by Elmore Leonard, the film won a Golden Globe for John Travolta (Best Actor in a Comedy or Musical). The film was also entered into the 46th Berlin International Film Festival. Following Tim Burton and the Coen Brothers, Sonnenfeld would tell stories about unusual, unorthodox people who are into the unexpected and the strange. He would use as his trademarks unusual camera angles, offbeat dialogue, and in certain films, strange behavior and weird creatures.

In 1996, Steven Spielberg asked him to direct Men in Black (1997). Starring Tommy Lee Jones and Will Smith, the film was a critical and financial smash. Producer Jon Peters then asked Sonnenfeld to direct Wild Wild West (1999), an adaptation of an old TV series. Wild Wild West was an expensive disappointment. He also directed the comedy Big Trouble (2002), after which he made his most successful film sequel to that point, Men in Black II (2002). He is also a contributing Editor for Esquire. He also co-produced the 2007 film Enchanted for Disney that starred Amy Adams. In 2008, Sonnenfeld earned an Emmy for directing Pushing Daisies. On April 21, 2010, it was announced that Sonnenfeld intended to return for Men in Black 3. The film, released in 2012 worldwide, received good reviews and became the highest grossing in the series.

In 2012, it was stated that he was appointed to direct Lore, an adaptation based on the comic by T.P. Louise and Ashley Wood of the same name. But, in 2013, Indie Director Dave Green has signed on to replace Barry Sonnenfeld as Director, Sonnenfeld will take part as executive Producer on the project.