Production notes

The Scooby-Doo franchise, which by the time of this film's release was nearing its 30-year mark, had entered into a period of diminishing returns in the early 1990s. After the conclusion of the sixth iteration of the series, A Pup Named Scooby-Doo, the character became absent from Saturday-morning lineups. In 1991, Turner Broadcasting System purchased Hanna-Barbera, the animation studio behind Scooby, largely to fill programming at a new, 24/7 cable channel centered on animated properties: Cartoon Network. The advent of cable gave the franchise renewed popularity: rapidly, Scooby reruns attracted top ratings. Zombie Island was not the first attempt at a feature-length Scooby adventure; several television films were produced in the late 1980s starring the character, such as Scooby-Doo and the Ghoul School. In 1996, Turner merged with Time Warner. Davis Doi, in charge at Hanna-Barbera, was tasked with developing projects based on the studio's existing properties. Warner executives suggested Scooby, given that the property held a high Q Score, and proposed it could be a direct-to-video feature film. The team assembled to work on the production were veterans of the animation business, and had most recently worked on SWAT Kats: The Radical Squadron and The Real Adventures of Jonny Quest. Screenwriter Glenn Leopold had been with the franchise since 1979's Scooby-Doo and Scrappy-Doo. The film was directed by Jim Stenstrum, who had worked on Scooby projects beginning in 1983's The New Scooby and Scrappy-Doo Show. As the film was considered a one-off experiment by studio brass, the crew worked with little oversight and complete creative freedom. Doi and Leopold developed the film's story, with Leopold receiving sole credit for the screenplay. Most of the script is recycled from Leopold's script for the unfinished SWAT Kats episode "The Curse of Kataluna". Stenstrum and Doi suggested in early story meetings that the monsters in the film be real (previous Scooby outings were nearly always "bad guys" in rubber masks), feeling it worked for a half-hour television episode, but might grow tiresome over a feature-length film. Leopold disagreed, noting that throughout the franchise's history, it always remained a simple, solvable mystery. Lance Falk, who worked as model coordinator on the film, suggested they combine both ideas.

Casey Kasem was originally set to reprise his role as Shaggy, but Kasem, a vegetarian, had refused to voice Shaggy in a 1995 Burger King commercial and went on to demand that Shaggy also give up eating meat in future productions. The creative team rejected this, as eating anything was a hallmark of the character. Additionally, production on Zombie Island had already begun, with the film featuring a scene with Shaggy eating crawfish. Shaggy was then recast with voice actor Billy West. Kasem was given a last-minute opportunity to fill the role and redub over West, but he made yet another refusal. Radio personality Scott Innes voiced Scooby-Doo, as Don Messick, the character's original voice actor, retired in 1996 and died in 1997; Zombie Island was subsequently dedicated to his memory. Heather North was also set to reprise her role as Daphne, but after a day of recording, Mary Kay Bergman replaced her, while B. J. Ward, who played Velma in a Johnny Bravo crossover episode, reprised her role for this film. Frank Welker is the only actor from the original series to reprise his role, as Fred Jones. Welker had initially worried that the producers would replace him as well, given that the producers believed his voice had gone down an octave; the voice director kept requesting Welker perform the voice at a higher pitch. Welker insisted his voice was the same, as Fred's voice is very close to Welker's natural speaking voice. The team went back and viewed early Scooby-Doo episodes and found that Welker's impression was more or less the same. Bob Miller, of Animation World Network, suggested that the reruns of Scooby-Doo aired on Cartoon Network perhaps gave the team a false idea of the character's voice, as the episodes were typically time-compressed (or sped-up) to allow more room for commercials, thus giving all of the show's audio a higher pitch.

Japanese animation studio Mook Animation were contracted to work on the film; Doi had a relationship with the team at Mook, as they had previously collaborated on SWAT Kats and Jonny Quest. Hiroshi Aoyama and Kazumi Fukushima directed the overseas animation, but are not credited on the picture. The film was animated and is presented in standard 1.33:1 full frame format. The team were allowed more time to work on the film, as there was no real set schedule—just delivery to the home video department upon completion. The American crew re-designed the series cast for the film, giving them a fashion update. The team felt Fred and Daphne, with their ascots and Fred's bell-bottoms, felt very dated to the '60s (although the original designs were used in the opening scene). Fred wore a pair of jeans, a baby blue dress shirt, and a khaki vest. Daphne is seen wearing a suit, consisting of a purple skirt and purple suit jacket, her undershirt is green in accordance to her original color scheme, her headband is removed as well. The team also briefly changed Shaggy's shirt color to red and gave him sneakers, though they quickly relented, as they viewed his original outfit as more timeless. Velma was also given very few changes, although her pleated skirt was replaced with a regular red skirt, her knee high socks are now rolled to the ankles and her shoes are sneakers, not the '60s styled Mary-Janes from her original design. Velma still sported an orange turtle neck sweater, and her color scheme was unchanged. The entire gang is seen in their original 1960s attire in the opening scene. The group were trusted by the studio's management as they had worked together for a long time, and all involved on the film had a real passion for the project. Drew Gentle was the main background designer for the project, with Falk contributing to the film's color key. Occasionally, the crew would hire freelance artists to contribute to ancillary designs. In addition, the group enlisted the assistance of Iwao Takamoto, the original designer of Scooby-Doo, still on salary at Hanna-Barbera, for advising on scenes. Takamoto called the film "a good solid mystery", and storyboarded several sequences of interplay between Shaggy and Scooby.

Composer Steven Bramson, who is known for Tiny Toon Adventures, JAG and the Lost in Space film, scored and conducted the film. The soundtrack for the film features three songs composed specifically for the film. "The Ghost Is Here" and "It's Terror Time Again", both written by Glenn Leopold, were performed by Skycycle. The title track, "Scooby-Doo, Where Are You!", was performed by Third Eye Blind.

The film has received widespread rave reviews after its initial release. On Rotten Tomatoes, the film holds an approval rating of 89% based on nine reviews, with an average taking of 8/10. Donald Liebenson of the Chicago Tribune described the film as "ambitious" and calls it "a nostalgic hoot [that] resurrects all the touchstones of the original cartoons." Entertainment Weekly's Joe Neumaier praised the film as "Fast, fun, and filled with knowing winks, the mystery honors the show’s beloved structure, but writ large." A 1998 New York Times article by Peter M. Nichols complimented the film as "well-made." Lynne Heffley at the Los Angeles Times called the film "more entertaining than you'd expect, despite the familiar Saturday morning-type animation." Retrospective reception have also been positive. Michael Mallory at the Los Angeles Times credited it and its subsequent features for "[spinning] the characters into more modern treatments of action and horror, and toyed with [a] self-spoofing quality." Mariana Delgado of Collider writes "a notable shift in tone and aesthetic departs from its source material [...] It's how the film injects the situation with enough realism to seem like a live-action horror film while still staying true to the animation." A 2022 Variety ranking placed Zombie Island as the best Scooby offering, with Carson Burton claiming "The film is at once extremely rooted in the classics yet willing to do something never seen before [...] The greatest of them all, Scooby-Doo on Zombie Island gets everything right."