He will star alongside Tom Cruise in the film, 33 years after the original was released, US media reported.
Filming for Top Gun: Maverick started at the end of May. It is being directed by Joseph Kosinski, who also directed the Tron sequel in 2010.
Kilmer appeared to confirm last year that he had cancer, and that he was "healing".
Cruise posted a photo on Twitter last week, referring to the first day of returning to the role of United States Naval Aviator Lieutenant Pete "Maverick" Mitchell.