Goddard began his career at The Walt Disney Company in 1974, as an original cast member of, and later directing, the Hoop-Dee-Doo Musical Revue at Walt Disney World Resort's Fort Wilderness. He then went on to work at Walt Disney Imagineering, where he developed concepts for EPCOT, Tokyo Disneyland, and River Country, among others.

Gary Goddard Productions, Goddard's first company, was formed in 1980, which became Landmark Entertainment Group in 1985. Goddard exited Landmark Entertainment Group in 2002 to start his new company, Gary Goddard Entertainment (now "The Goddard Group"). Goddard created several large-scale attractions for Universal Studios, including The Amazing Adventures of Spider-Man (at Islands of Adventure, and Universal Studios Japan), Terminator 2/3D: Battle Across Time (at Universal Studios Florida, Universal Studios Hollywood, and Universal Studios Japan), Jurassic Park: The Ride (Universal Studios Hollywood, Islands of Adventure, and Universal Studios Japan), Conan: A Sword and Sorcery Spectacular (Universal Studios Hollywood), and Kongfrontation (Universal Studios Hollywood).

Goddard directed the 1987 movie Masters of the Universe.

Other notable attractions created by Goddard and team include Star Trek: The Experience (Las Vegas Hilton), The Georgia Aquarium (Atlanta, Georgia), and Sanrio Puroland (Tokyo) and Harmonyland (Kyshu Island) in Japan. For Six Flags, Goddard is responsible for the creation of the Monster Plantation dark ride at Six Flags Over Georgia, as well as its 2009 makeover into Monster Mansion. Goddard also oversaw the creation of the Glow in the Park Parade (playing at Six Flags Great Adventure beginning in 2008, Six Flags Mexico beginning in 2008, Six Flags New England beginning in 2008, Six Flags St. Louis beginning in 2009, Six Flags Over Texas beginning in 2009, and Six Flags Great America beginning in 2010). Goddard also was responsible for the conceptual development of Six Flags Dubailand and Six Flags Qatar.

In April 2014, Goddard and his frequent film collaborator Bryan Singer, along with several other filmmakers, were sued by actor Michael Egan III, who alleged that they had sexually assaulted him when he was a minor and had videotaped some of the assaults. Egan withdrew his lawsuit against Goddard in June 2014; by August of that year, he had dismissed his lawsuits against all of the other defendants as well.

On November 10, 2017, actor Anthony Edwards wrote an essay on Medium in which he alleged that Goddard molested him and raped his best friend "for years" starting when they were 12 years old. Speaking on behalf of Goddard, his publicist denied the allegations.