The film is inspired by the murder of voting rights activists James Chaney, Michael Schwerner, and Andrew Goodman by the Ku Klux Klan.
Gene Hackman decided that he would no longer make violent films after seeing a brief, violent clip of his performance in this film (taken out of context, in his eyes) at the 1989 Oscars. That stance prevented him from accepting a job as director of The Silence of the Lambs (1991) and almost cost him the Sheriff role in Unforgiven (1992), which he reluctantly accepted after Clint Eastwood convinced him. That role that earned great acclaim, and his second Oscar.
The name "Mississippi Burning" was the name of the actual FBI case that was abbreviated MIBURN.
In a review for Radio Times, former BBC film critic Barry Norman described the film's opening as "pure cinema, something no other medium could do so effectively."
The film doesn't mention that the Navy men who searched the swamp found the bodies of eight more murder victims, including college student civil rights workers Henry Hezekiah Dee and Charles Eddie Moore, who had disappeared one month before Chaney, Goodman, and Schwerner. As indicated in the film, the method of murder used by the Klan and law enforcement was well-organized and had been done before.