Back when the movie was in the pre-planning stages, the story was supposedly going to revolve around the GS Ball, which Ash and company carried all throughout the Orange Islands and 1/3 of the way through Johto. Evidentally, the GS Ball was going to be finally opened to reveal that Celebi was hidden inside. This may have been the movie's plot had Pokémon Crystal not come out for the GameBoy Color.

Because Miramax is now the distributor (and maybe because of the lower budget), the original Japanese score is used in this film (except during the three US-only scenes). In the previous movies, all the music was changed, as is now being done on the TV series.

In the early reports when Movie 3 was still being made, there were rumors that Movies 3 and 4 were going to be interconnected, with Entei working with Mewtwo or something and then finding Celebi. Obviously, the creators abadoned this idea.

Because of the new scenes, this movie came out long after the Pokémon craze and very long after the previous movie. To compensate, Miramax placed "The World of Pokémon" in front of both this movie and the next one. The segment was originally an extra on the DVD to Mewtwo Strikes Back and is basically for the unintiated to know what is going on.

There was one scene cut out of the English version. At the end, when Celebi transports Sammy back to his own time, the Japanese version actually shows him landing in his own time, and having Diana's grandmother giving him his sketchbook back, saying he had a wonderful dream.

When 4Kids adapted the movie for English audiences, it actually paid the Japanese producers to animate three new scenes, which is why it took so long for it to come out in the U.S. The first new scene is when Professor Oak is explaining Suicune's powers to Ash in the beginning. Originally, it had Tracey and Ash's Muk in the background, but in the new one it doesn't. The second new scene is when Team Rocket tries to grab the peach from Vicious's mech and fall off. The final piece is at the end when Ash tells Professor Oak the story and basically shoves the whole "Sammy is Professor Oak" subplot down the people's throats. In the Japanese version, the only clue you had was during the end credits, when Tracey finds Sammy's old sketchbook in Professor Oak's closet.