Gina Philips (Trish) and Justin Long (Darry) were not allowed to meet Jonathan Breck before filming (in order to get a true reaction from them when they actually did see him with his full costume and makeup), nor did they see the BEATNGU truck before the opening scene was shot. When Philips first saw the truck, she said something to the effect of: "Is that the truck? Jeepers, that's creepy."
The scene where Trish and Darry witness the Creeper dumping a body down a well by an abandoned church was inspired by the case of Dennis DePue, a former Michigan Property Assessor who murdered his wife and was seen by witnesses near an old school house with a bloody sheet. Two witnesses also recall DePue speeding past them in a van and eventually tailing them and riding their bumper for several miles. The case was also profiled on a 1990 episode of Unsolved Mysteries (1987).
Director Victor Salva wanted the countryside settings for the film to have an eerie quality about them. However Salva said that the Florida filming locations were so beautiful that often times the footage for the film would have to be darkened down to give the locations a more menacing appearance.
The oath "Jeepers Creepers!" originated in the early 20th century as a polite euphemism for Jesus Christ. Jiminy Crickets was a synonym before the latter phrase was co-opted by Walt Disney as the name of a cartoon insect.
(at around 1h 2 mins) When Darry is looking at the missing person posters in the police station there are several comedic comments such as Tim Sullivan's hair being "dusty beaver" and his occupation being "a butcher a baker and a candlestick maker" among others.
at around 56 mins) The Creeper originally had one line of dialog in the film. After he kills the old cat lady and holds her body upright, revealing his true face to Darry and Trish, he originally said "She don't smell too good, Darry..." before tossing her corpse aside. This line was cut and replaced with silence as the producers thought it would be more effective to have the Creeper say nothing. Still, you can see The Creeper's lips move in sync with the line if you look closely.
at around 2 mins) In the beginning of the film, Darry tells Trish that she once actually did something decent for him and that's a part of history she can't change. This is a strong allusion to the ending of the film where Trish tries to give her life for Darry's, but ultimately fails.
In the end of the film when Justin Long's character, Darry, is heard screaming, it is actually Tom Tarantini, who also had the minor role of car thief Austin McCoy as well as Coach Dwayne Barnes in Jeepers Creepers II (2003). Tarantini stood in for Long, as he was busy shooting Season 2 of Ed (2000), while this scene was filmed.
at around 1h 14 mins) When Trisha and Darry first meet Jezelle, she reveals that she hears one of them screaming in the dark. Darry is frantically asking her who she hears. Jezelle turns to Trisha, and the audience is led to believe it's her. However, towards the end of the film, you can plainly tell it's a man screaming. Jezelle may have looked at Trisha because she could tell how scared Darry already was, and simply didn't know how to tell him that his screams were the ones she heard.
In the screenplay ending, Darry does not scream as the camera moves through the factory. The camera pans through the place until finally the camera is in the basement. Darry's eyes are sewn shut and he is added to a display of other dead bodies.