This film was originally set to have a much darker tone, essentially poking fun at the original series, and was set for a PG-13 rating. Shaggy was set to be a stoner, Velma and Daphne had a side relationship, and there were many marijuana references. But Sarah Michelle Gellar said, after the cast had signed on, there was a change and the film became more family-friendly.
The director, Raja Gosnell wanted a real life couple to play Daphne and Fred. His first choice was Sarah Michelle Gellar and Freddie Prinze Jr. Prinze Jr. didn't originally want to do the movie because he felt it wouldn't live up to the Scooby cartoon, but Gellar talked him into it.
Sarah Michelle Gellar had to film Scooby-Doo around her already hectic Buffy the Vampire Slayer (1997) schedule. The producers of both productions arranged it so that she would spend two weeks in Los Angeles shooting Buffy, then the next two weeks in Queensland, Australia filming Scooby-Doo.
In the scene where Fred, Velma and Daphne meet up at the airport, there was originally a flashback for each of them showing what they had all been doing: Fred on a book tour, Velma in a support group and Daphne learning Martial Arts. The flashbacks were cut out because the director thought they dragged out the scene.
Frank Welker, who has voiced Freddy Jones in all the Scooby-Doo cartoons, provides his voice to one of the evil creatures in this movie. From 2002 Welker has also taken on the job of voicing Scooby-Doo.
Shaggy is a strict vegetarian in this film. Casey Kasem, Shaggy's original voice actor, insisted that Shaggy become a vegetarian during production of Scooby Doo, Where Are You! (1969), though this was not always the case in various spin-offs.
Originally, Matthew Lillard would scream for a very long time to make his voice all hoarse to do a perfect Shaggy imitation. It didn't work out, so he began trying to imitate the voice he did when his voice was all tired out from all the screaming.
The scenes filmed in Australia where filmed at Bond University, in the Gold Coast, which is known to have perfect weather 350 days a year. Unfortunately, Velma (Linda Cardellini) got a cold, and filming had to be stopped for a day.
The idea of a Scooby-Doo movie languished in "development hell" throughout most of the 1990s. In 1996, Jim Carrey was attached to play Shaggy and Sara Gilbert was attached to play Velma. At one point, director Kevin Smith was attached, but later dropped out. Later, Mike Myers accepted the project and was the one who most often had his name linked to it (Myers' friend Janeane Garofalo was supposedly tapped by Myers to play Velma). Eventually, even Myers had to leave the project.
There was an alternate animated opening, showing the cartoon versions of the characters but it was cut for time. This sequence also featured a rendition of the Scooby Doo, Where Are You! (1969) theme by artist Shaggy, part of which appears in the final film.
Originally, Scrappy Doo was the not going to be the main villain. At the end of the film, Old Man Smithers aka "the Luna Ghost" from the beginning of the movie was going to be behind the event of the film.