A bunch of Pteranodons appear in The Rite of Spring segment in Fantasia. They are seen flying over head trying to catch prey in the ocean. Two of them were fighting over a squid and one, with a fish in his mouth, gets dragged into the water by a Tylosaurus, causing him to drown. They are never seen again for the remainder of the segment but presumably died out with the other dinosaurs in the mass extinction.
One Pteranodon is seen picking up Aladar's egg from the water and flying towards Lemur Island to feed its children, only to get stopped by two birds, causing it to drop the egg into the island. The species shown in this movie is Pteranodon sternbergi, which some scientists think is a different creature called a Geosternbergia, a close relative of the Pteranodon.
The Pterandon appears in the episode "Dino World", along side the Ankylosaurus. They are discovered to exist on another planet along many other earth dinosaurs. At the episode's climax, three Pterandons chase the Callistos away after Loretta wakes up an Ankylosaurus.