Chris Carter was born on October 13, 1956 in Bellflower, California. His father worked in the construction industry. Carter has described his childhood as "fairly normal", and was fond of both Little League Baseball and surfing; his surfing stance is goofy footed. He attended California State University, Long Beach in Long Beach, graduated with a journalism degree in 1979. An avid Surfer, he began writing for Surfing Magazine, a San Clemente-based journal, eventually becoming its Editor at the age of 28. Carter would work for the magazine for thirteen years, and credits his tenure there for teaching him how to run a Business. It was also at this time that Carter began taking an interest in pottery, making "hundreds of thousands of pieces" of dinnerware as a hobby. He has compared the process of making pottery to Zen meditations, although he has since thrown out most of his work.

In 1983, Carter began dating Dori Pierson, whom he had met through a cousin of hers who worked with him at Surfing Magazine. Pierson's connections at Walt Disney Studios led to chairman Jeffrey Katzenberg hiring Carter on a standard contract. Carter began writing television films for the studio, penning The B.R.A.T. Patrol in 1986 and Meet the Munceys in 1988. These scripts led to Carter being associated with contemporary youth comedy at the studio, and although he enjoyed the work he felt that his real strengths and interests lay in serious drama instead.

Peter Roth, at that time the President of Stephen J. Cannell Productions, obtained a copy of Carter's pilot script for Cool Culture, and although the series was never picked up, Roth was interested in hiring Carter to work on the CBS series Palace Guard. However, Roth would soon leave CBS to work for Fox as the head of its television production wing. Carter was among the first wave of new staff hired by Roth in 1992 to develop material for the network, and he began work on a series based on his own childhood fondness for The Twilight Zone and Kolchak: The Night Stalker.

During the production of the fourth season of The X-Files, work on the first feature film adaptation of the series began. Also titled The X-Files, Carter initially began a treatment for the script over Christmas holidays in Hawaii in 1996. Series Producer Frank Spotnitz collaborated on the story outline at this time. Carter would later return to Hawaii for a ten-day stint in 1997 to begin fleshing out the finished script. Carter appointed frequent series Director Rob Bowman as Director of the film, which went on to feature many of the series' regular cast, including Duchovny, Anderson, Mitch Pileggi and william B. Davis.

The X-Files premiered on June 19, 1998, eventually making a worldwide gross of $189,176,423. The film currently holds a rating of 60 out of 100 on review aggregation website Metacritic, based on their weighted average of 23 reviews. Fellow review aggregation site Rotten Tomatoes rates the film 64%, based on their analysis of 69 reviews.

In 1999, Carter began adapting the comic book series Harsh Realm as a television show, also titled Harsh Realm. Carter's friend and frequent collaborator Daniel Sackheim had optioned the comics for adaptation in 1996. However, when the series first aired on October 8, 1999, the comics' Writers Andrew Paquette and James Hudnall were given no writing credits for the work; the two then filed suit against Fox to be credited for their work. Harsh Realm received disappointing viewing figures, and was cancelled after only three episodes had been broadcast.

Ten years after the success of the first film, and six years after The X-Files final season had finished, Carter would both write and direct a second feature film, titled The X-Files: I Want to Believe. Filmed in British Columbia, I Want To Believe was released on July 25, 2008; eventually grossing $68,369,434 worldwide. The film was received poorly by critics, holding ratings of 32 and 47 on Rotten Tomatoes and Metacritic respectively.

Two years later, Carter launched a spin-off of The X-Files titled The Lone Gunmen, a series centred on three minor characters from the former series. The Lone Gunmen was cancelled after thirteen episodes, later receiving a coda in the form of a crossover episode with The X-Files. Carter has since been involved with writing and directing the as-yet unreleased film Fencewalker, set to feature Natalie Dormer and Katie Cassidy. In 2011, he began working to develop Unique, a police thriller television series; the project was eventually dropped before completion.

After finding the series' two starring leads in Gillian Anderson and David Duchovny, Carter was given a budget of $2 million to produce a pilot episode. The series aired on Friday nights on the Fox network, being broadcast in tandem with The Adventures of Brisco County, Jr. in what was perceived to be an unpopular timeslot. The series earned relatively impressive Nielsen ratings for its Friday timeslot, and was given a full twenty-four episode order. The series' popularity and critical acclaim built over the course of its second and third seasons, and saw it earning its first Golden Globe Award for Best Television Series – Drama and breaking the record for highest price paid by a network for rights to air re-runs, fetching $600,000 per episode from Fox's sister network FX. After Carter's initial three-year signing for Fox had ended, the success of the series allowed him to negotiate a five-year contract with several additional perks, including the guarantee of a feature film adaptation to be produced by the parent company's film studio, and the greenlighting of Carter's next television project. In March 2015, it was confirmed that Carter is set to executive produce and write the screenplays for the revival of The X-Files, which is set for a six-episode event series.

Carter next began work on the Amazon Studios television series The After. The pilot episode was made available for viewing on February 6, 2014; the series was green-lit the following month, but finally cancelled on January 5, 2015, without another episode beyond the pilot being shot.