In 1990, his first writing credit was for Death Warrant, a low-budget action film starring Jean-Claude Van Damme. A year later he wrote Kickboxer 2: The Road Back, a sequel to the Van Damme film released two years prior, directed by Albert Pyun without Van Damme's involvement. Also in 1991, Goyer did an uncredited polish on the script to Pet Sematary II.[citation needed]

Goyer's next two films, Demonic Toys and Arcade (the latter again directed by Pyun) were produced by Full Moon Features.

Goyer wrote several drafts for The Puppet Masters, based on a novel by Robert Heinlein; the film's complicated development became the subject of an article by Terry Rossio, who penned the initial drafts with collaborator Ted Elliott.

Goyer was hired to write a sequel to The Crow, called The Crow: City of Angels. Alex Proyas, director of The Crow, hired Goyer to write a polish for his next film, Dark City.

In 1997, Goyer co-created and served as executive producer for the short-lived science-fiction series Sleepwalkers.

Goyer's first adaptation of a Marvel Comics character, Nick Fury: Agent of S.H.I.E.L.D., was produced in 1998 as a television movie with David Hasselhoff in the lead role.

His next work with Marvel, released in the same year, was Blade. Goyer created the original character of Whistler, Blade's mentor, for the film. The character was later added into the comic book's continuity.

Goyer wrote screenplays based on numerous comic book series, among them Silver Surfer, Doctor Strange, Ghost Rider, Batman, and Sub-Mariner. Most have yet to be filmed.

For DC Comics, Goyer wrote a title based around the Justice Society of America. JSA debuted in August 1999, with Goyer's involvement lasting four years, ending with issue 51. Unfamiliar with the structure of a comic script, Goyer would outline the issues before working with a professional comic book writer on the final script.[citation needed] For the first five issues he collaborated with James Robinson and, for the rest of the series, with Geoff Johns, who would take over as solo writer following Goyer's departure.

In 2000, Goyer produced Mission to Mars, directed by Brian de Palma. The film did not recoup its US$90 million budget.

2000 also saw the debut of FreakyLinks, on which Goyer served as executive producer (he also wrote an uncredited polish of the pilot episode[citation needed]).

In 2002, Goyer served as writer and executive producer for Blade II, a sequel to the 1998 film written by Goyer. Directed by Guillermo del Toro and with designs and storyboards by artist Mike Mignola (who would later collaborate with each other on Hellboy), the film outgrossed its predecessor.[citation needed] The same year, Goyer made his directorial debut on ZigZag, his own adaptation of a novel by Landon J. Napoleon. The film received a limited theatrical release.

In 2004, Goyer served as writer, producer, and director on Blade: Trinity. The film failed to make back its budget at the box office.

In 2005, Batman Begins was released. Goyer wrote the first draft of the script for director Christopher Nolan after collaborating on the story together. Batman Begins went on to make over $200,000,000 at the domestic box office.

Also in 2005, the television series Threshold premiered. Created by Bragi F. Schut, the series was produced and developed by Goyer, who also directed the pilot. The series was cancelled part way through the first season.

Blade: The Series premiered in 2006. Developed and executive produced by Goyer with his JSA writing partner Geoff Johns, it was cancelled after the first season.

In 2006, Goyer was interviewed by producer Mike De Luca for The Dialogue DVD series. Goyer discusses his methods and experiences as a screenwriter.

A sequel to Batman Begins is in the works, titled The Dark Knight. Goyer is slated to write the outline, with Nolan writing the final script with his brother Jonathan.[citation needed]

February 2007 saw the release of Ghost Rider. Based on the Marvel comic, the script was written several years prior by Goyer,[citation needed] who also serves as executive producer. The final script was written by director Mark Steven Johnson.

Goyer had been working on an adaptation of The Flash, but he has left the project since he and Warner Brothers could not come to an agreement on the story.

Goyer has also written the working treatment for the film adaptation of Marvel's Thor, as well as directing the X-Men spin-off, Magneto. He also directed The Invisible, a film that was released on April 27, 2007.