Noah Hathaway was hurt twice during the making of the movie. During his horse riding training he was thrown off a horse which then stepped on him. Then during the shooting of the drowning sequence in the "swamp of sadness" his leg got caught on the elevator and he was pulled under water. He was unconscious by the time he was brought to the surface.
Noah Hathaway almost lost an eye during the fight-scene versus Gmork. One of the claws on his giant paws poked him in the face. The robot was also so heavy that he lost his breath as well when he was hit to the ground by it. They only made one shot due to the risk that he would get seriously wounded.
Two scenes from the book were written in the script but ultimately scrapped due to special effects limitations. The first was the initial appearance of Falcor, where Atreyu rescues him from Ygramul the Many, a swarm of poisonous wasps taking the form of a giant spider. This is where Bastian's scream being heard by the characters in the book was to have taken place, and also explained why Atreyu and Falcor are later seen being given medicine by the Gnomes. The second cut scene involved Atreyu and Falcor encountering the Wind Giants, giant creatures made of clouds, and being caught in a fight between them. This was re-edited into their close encounter with the Nothing before Atreyu falls into the sea.
The Night Hob says a profanity in the opening scene where the Rockbiter appears running down all in its path. This profanity is often dubbed over by the grumble of the Rockbiter's scooter, so that it can be shown as a children's film.
The name of the mystical land in (the English translation of) the original novel was Fantastica, not Fantasia, but the original German name Phantásien translates more accurately into English as Fantasia.
During filming in Germany, because it was an unusually hot summer one of the statues of the Ivory Tower actually melted. On other days, the crew were forced to shut down production because the blue backgrounds for the matte work refused to operate properly.
Tami Stronach was attending theatre classes in San Francisco when she got the audition to be The Childlike Empress. Her acting teacher was friends with the production executive and talent scout Anna Gross. Tami initially believed she was auditioning for a little play and had no idea it was to be for a major motion picture.