Since Gorillas in the Mist (1988), Rick Baker stated that he wouldn't do any more projects that involved creating animatronic apes. Baker had to break that statement when he did Baby's Day Out (1994), which featured a gorilla scene. After that, Baker restated he would not do any more ape projects, but when he got called to work on this movie, Baker's love for the original film changed his mind. He also saw it as a chance for redemption for King Kong (1976) since he designed the King Kong suit and portrayed Kong himself. This movie was the last for which Baker created an animatronic gorilla suit. He later added Planet of the Apes (2001), starring Mark Wahlberg, to his ape-centric résumé.
Like most 90s movies that featured creature effects, a mix of practical and digital effects created Joe Young. Creature suit performer John Alexander, who wore a radio-controlled animatronic gorilla suit made by special makeup effects artist Rick Baker and his crew at Cinovation Studios, portrayed Joe for most of the film. Verne Troyer played Joe as an infant in the opening.
Bill Paxton's character's name Gregg O'Hara is a combination of Ben Johnson and Robert Armstrong's characters Gregg and Max O'Hara from Mighty Joe Young (1949).
On July 2, 1997, during filming in the San Fernando Valley, director of photography Donald Peterman and camera operator Ray De La Motte were injured after the Panther Pegasus camera crane on which they were riding snapped, causing them to fall twenty-five feet to the ground. Peterman suffered a broken leg, broken ribs, and minor head injuries, and De La Motte received minor chest and back injuries. Production was halted for two days, and Peterman was replaced by Oliver Wood. In 2000, Peterman sued Panther, as well as Shotmaker Company, the crane's supplier, and won a $5 million settlement.
Terry Moore, Ray Harryhausen: The star of Mighty Joe Young (1949) and the legendary stop-motion animator, who did most of the 1949 movie's animation, appear as an elderly couple at the gala. Looking at Jill Young, Moore states, "She reminds me of somebody, but I can't think who." Harryhausen replies, "You, when we first met."