Aerodactyl's first appearance in the show was in the episode "Attack of the Prehistoric Pokemon." It scared off the other prehistoric pokemon that were chasing Ash and Team Rocket. It then kidnapped Ash who was saved when his Charmeleon evolves into a Charizard.
Fossils of Aerodactyl and Kabutops were resurrected by Annie and Oakley in Pokemon Heroes. These Pokemon were once owned by an evil trainer to torment the civilians of Alto Mare, but were drowned when Latios brought water to the city. They were sent to chase after Ash and Latias and blank, yellow tinted eyes with no pupils and are lined with a thick black outline.
In the episode "Putting the air back in Aerodactyl" Gary Oak revives an Aerodactyl that enjoyed pear-like fruits that grew in the forests of an island. Butch and Cassidy attempted to steal it and present if to Dr. Namba, but were stopped by Gary's Umbreon and Dodrio along with Aerodactyl who sent the Team Rocket agents flying with a hyper-beam.