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 cartoons, but Gellar talked him into it.
This film was originally set to have a much darker tone, essentially poking fun at the older cartoons, 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. According to Sarah Michelle Gellar, after the cast had signed on, there was a change and the film became more family-friendly. However, by 2017, James Gunn confirmed that the original cut of the film got an R-rating and had to use CGI to cover cleavage.
Neil Fanning was on set every day to provide Scooby's dialogue for the cast to interact with. This led to him and Matthew Lillard becoming close friends, as they had to be very inventive to make Shaggy and Scooby's friendship convincing (since Lillard was acting with nothing there except Fanning's voice off-screen).
When Daphne attempts to recruit Shaggy and Scooby to inspect the castle with her, Shaggy objects. He says: "Like, Scoob and me don't do castles. Because castles have paintings with eyes that watch you, and suits of armor you think is a statue with a guy inside that follows you every time you turn around!" Everything that Shaggy describes, occurred in What a Night for a Knight (1969), the very first Scooby-Doo cartoon to be aired.
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.