Goyer was born and raised in Ann Arbor, Michigan. He is Jewish and an alumnus of Huron High School and the University of Southern California, graduating from the School of Cinema-Television in 1988.
Goyer was a student of screenwriter Nelson Gidding at USC and frequently returned to Gidding's class as a guest speaker. He graduated in 1988 and sold his first screenplay for Death Warrant in 1989. With his first paycheck, he bought a new Isuzu Trooper, which was stolen the very first night he drove it home.
Goyer has written several screenplays based on numerous comic book series, among them Doctor Strange, Ghost Rider, Batman Begins, The Dark Knight, The Flash, and Blade.
Goyer wrote a title based around the Justice Society of America for DC Comics titled JSA, which debuted in August 1999. For the first five issues, he collaborated with James Robinson and, until his departure following issue 51, with Geoff Johns, who would take over as solo writer.
Goyer is co-creator with Brannon Braga of FlashForward, a science fiction TV series that premiered on ABC in Fall 2009. The show is based on the novel by Robert J. Sawyer. He stepped in as show runner in October 2009 after the show struggled out of the gate. On Feb. 5, 2010, Goyer announced he would be stepping down as FlashForward showrunner to focus on feature films and directing. Replacing him as showrunners are Jessika Borsiczky, Lisa Zwerling and Timothy J. Lea.
Goyer is currently working on writing the upcoming Superman film, and the third installment of Christopher Nolan's Batman film series.