Wong was born in British Hong Kong, and moved to the United States along with his family at age 10 to San Diego, California. During his youth, he met his future writing partner Glen Morgan at El Cajon Valley High School. Later on, he went to Loyola Marymount University, joining a comedy improv group. Originally seeking a major in engineering, he later switched to a film major after seeing Apocalypse Now at the Cinerama Dome. After graduating, he landed a job as an assistant to Sandy Howard. During this time, both Wong and Morgan wrote screenplays, eventually having one produced.

With Morgan, he co-wrote The Boys Next Door. After this Wong became a story editor on the short-lived ABC crime drama Knightwatch. Later, with Morgan, Wong would work on many Stephen J. Cannell productions, including Wiseguy (as supervising producer), The Commish (as supervising producer), and as a staff writer and story editor for 21 Jump Street and its spinoff, Booker.

Wong and Morgan began working with Chris Carter on the science fiction/drama The X-Files, about two FBI agents investigating the paranormal, filmed in Vancouver.

In 1995, Wong and Morgan were offered an $8 million, four-year contract deal with 20th Century Fox Television to write and produce television series. As part of this deal, Morgan and Wong went on to create the short-lived series Above and Beyond.

They returned to The X-Files briefly in its fourth season (1996—1997) when they wrote the horror episode "Home." Wong also made his television directing debut with the conspiracy-themed "Musings of a Cigarette Smoking Man," written by Morgan. Wong and Morgan also took on production and writing duties for Carter's Millennium. Later, they would go on to executive produce the short-lived NBC paranormal series The Others.

In 2000, Wong directed Final Destination, a film he co-wrote with Glen Morgan. Wong followed the directorial debut with The One (2001), an action film starring Jet Li, and with more horror films, including Willard (2003), directed by Glen Morgan and starring Crispin Glover, and a second sequel, Final Destination 3 (2006). In late 2006, Wong and Morgan's remake of Black Christmas was released; the script was by Wong and Morgan and the film was directed by Morgan. Wong has recently finished directing the live-action adaptation of the popular media franchise Dragonball.

James Wong is married to Teena Wong, with whom he has three children. They reside in California.