The film is inspired by the murder of voting rights activists James Chaney, Michael Schwerner, and Andrew Goodman by the Ku Klux Klan.
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."
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.
The news interview clips were filmed by Alan Parker, with real locals from Mississippi, and their lines were ad-libbed with only minor prompting. Parker said it uncomfortable at times because he wasn't always sure they didn't believe what they were saying.