Winter was born in London, England, to mother Gregg Mayer, a New York-born American who was a former Martha Graham Dancer who founded a modern-dance company in London in the mid-1960s, and father Ross Albert Winter, an Australian who danced with Winter's mother's troupe. Winter received training in dance as a child. He grew up in a Jewish family. He has an older brother named Stephen.

When Winter was five, his family moved to Missouri, where his father ran the Mid-American Dance Company, while his mother taught dance at Washington University in St. Louis. The two divorced in 1973.

In 1978, Winter moved to the New York City area, where he and his mother lived in Montclair, New Jersey. During this time Winter began performing as an actor on and off Broadway, commuting into New York City.

He became interested in the Internet in the late 1980s. Winter said he began devoting a lot of his attention to the Internet not just because he liked Technology, but also because "I found this community there." Winter liked the idea of large numbers of anonymous users discussing a variety of topics in an anonymous space. "I found that really striking then. And it seemed liked the beginning of something," he said.

In 1983, after graduating from Montclair High School, Winter was accepted into the Tisch School of the Arts at New York University. While at NYU, he met fellow aspiring filmmaker Tom Stern. The two collaborated on a number of 16mm short films and both graduated with honours.

In 1989, Winter found international success when he co-starred with Keanu Reeves as Bill S. Preston in the smash-hit comedy Bill & Ted's Excellent Adventure and its 1991 sequel, Bill & Ted's Bogus Journey.

Following the success of Bill & Ted, Winter and creative collaborators Tom Stern and Tim Burns were hired to develop a Sketch comedy show for MTV. The result, 1991's The Idiot Box, was a success for the network, but the channel's budgetary problems prevented them from filming additional seasons, and it was canceled after six episodes. Winter, Stern and Burns accepted a $12 million deal from 20th Century Fox to film their own feature film, which would end up becoming 1993's Freaked. While the film was never widely released, despite positive reviews from The New York Times, and Entertainment Weekly, Freaked went on to become a cult favourite, through festivals, TV and DVD, and was cited by Entertainment Weekly, on their list of Top Ten Comedies of the Nineties.

Winter was married to Sonya Dawson with whom he had a son, born in 1998. At some point, he and Sonya divorced. In 2010, he married Ramsay Ann Naito. They have two children.

Winter did not return to directing until 1999, when he filmed Fever. The film was shown at film festivals worldwide, including Official Selection in the Director's Fortnight at Cannes. New York Daily News praised the film, calling it "a claustrophobic mind bender. Winter sustains an aura of creepiness worthy of Roman Polanski."

Winter directed the live-action adaptation of the hit Cartoon Network series Ben 10, which aired in November 2007 and garnered the highest ratings in Cartoon Network history. He directed its sequel, Ben 10: Alien Swarm which aired on Cartoon Network in November 2009 and captured over 16 million viewers in its premiere weekend. He has reportedly been chosen to write the screenplay for the Howard Stern-produced remake of Rock 'n' Roll High School. His latest project is a 3D-remake of the 1987 horror film The Gate which was scheduled for release in 2011.

In April 2011, Winter's Bill & Ted co-star Keanu Reeves confirmed that a third installment of the film series was underway. Winter's confirmed work on Bill & Ted 3 was still in progress in a 2014 article on the original film's 25th anniversary. In 2016, Winter said that he hoped the film would go into production in 2017. Reeves confirmed in February 2017 that the third film is being made, and the Writers have a story. "Basically, they’re supposed to write a song to save the world and they haven’t done that" Reeves said about the plot of the movie.

Winter's interest in Technology, the Internet and privacy inspired him to make the 2012 documentary film Downloaded, about internet file sharing and Napster, and the 2015 film Deep Web, about the Silk Road, bitcoin, and the dark web.

In 2013, he had a role in the thriller Grand Piano, starring Elijah Wood and John Cusack, playing The Assistant.

In July 2015, Winter began work on a biographical documentary of the rock Guitarist and Composer Frank Zappa. The Zappa Family Trust publicly gave its approval to Winter's plans for the film. The Kickstarter campaign for this project was the highest funded documentary in crowdfunding history.

In 2016, Winter released a short documentary entitled Relatively Free about Journalist Barrett Brown's release from prison. This was followed by another short documentary, Trump's Lobby, about President elect Donald Trump.

On Friday, February 2, 2018, Winter revealed that he was molested by an older man at age 13 while he was acting on Broadway.

Winter’s 2012 VH1 Rock Doc Downloaded earned worldwide critical acclaim at theatrical and festival screenings. Winter's multiple award-winning 2015 documentary Deep Web, had its world premiere at SXSW and a broadcast premiere in the U.S. on the Epix network alongside a global festival tour. The film went wide on September, 2015, opening as the #1 documentary on iTunes.