After filming of final shootout was done, director Walter Hill was told to include more of it so he went back and shot more footage but in the end he cut it down because, in his words, "it got too big". This is probably why this scene has some continuity mistakes which are often thought to be caused by cuts made on violent scenes in order to avoid X rating.
The title comes from a line of dialog written in the script. The line "terminate with extreme prejudice" first appears on film in Apocalypse Now (1979) (although it originates in the Bernard Conners novel "Don't Embarrass the Bureau"). Both films were written by John Milius.
Funeral scene of sheriff Hank Pearson (Rip Thorn) was deleted after first two screenings of the movie. Soundtrack release for the movie does however includes track called "The Funeral" which was composed by Jerry Goldsmith for that deleted scene.