Noctowl debuted in Fowl Play!, where it flew to a birdhouse. Dr. Wiseman was trying to capture the Noctowl using traps rather than Poké Balls, but each time Noctowl outwitted him and escaped the traps — usually leaving him hypnotized in the process. Ash was offended by Wiseman's tactics and plotted to capture Noctowl traditionally. Wiseman hypnotized Noctowl using its own Hypnosis and a mirror, but Noctowl managed to escape — just in time for Team Rocket to attack and attempt to capture it. Ash risked his own safety to pry Team Rocket's mecha claw open and allow Noctowl to fly free, before Noctowl marshaled the power of Totodile, Cyndaquil, and Pikachu to destroy the mecha and send Team Rocket blasting off. Following the rescue, Noctowl challenged Ash to a battle. Dr. Wiseman decided that it was too smart for him to catch, so Ash should have a go. Pikachu was hypnotized and began to use Thunderbolt on everything except Noctowl. When he shocks himself, he returns to normal. Cunningly, to avoid further hypnosis, Pikachu closed his eyes and listened for Noctowl's wings, then used Thunderbolt, knocking Noctowl out and allowing Ash to capture it.
Noctowl (right) with a wild normal Noctowl (left)
In Carrying On!, Noctowl used its Hypnosis on a Fearow to make it believe it was a Charizard, causing it to flee in fear. It then used Hypnosis on the traumatized Pidgey victim, making it appear as a fellow Pidgey and allowing it to approach. Noctowl later led the gang to the lost carrier Pidgey that had been captured by Team Rocket and alongside Ken, the Pidgey it rescued before, freed them and led the Pidgey into an attack on Team Rocket's balloon.
Noctowl rotating its head
Noctowl was the Pokémon Ash based his Ecruteak Gym campaign around in From Ghost to Ghost. It successfully used Foresight on Gastly, but had to be recalled because it couldn't land any other attacks. It was then sent out against Haunter, struggling to overcome the Ghost type but managed to win through learning Confusion. It was then left to battle Morty's Gengar which was still fresh, and looked vulnerable as Gengar was able to attack while invisible. However, Noctowl was able to reveal Gengar's location by using Confusion through the whole building and then using Foresight to keep Gengar visible. It then finished Gengar off with a Tackle attack and Ash got the Fog Badge.
Ash briefly transferred Noctowl to Professor Oak in Ring Masters so that Oak could study its unique coloring while Ash borrowed his Snorlax.
In Throwing in the Noctowl, Ash sent out Noctowl and used its ability to fly in order to carry a plane headed for Olivine City.
In Fangs for Nothin', Ash used Noctowl in battle with Clair's Kingdra. Noctowl managed to land a Confusion attack, but an attempt to telekinetically levitate Kingdra was broken by a Hydro Pump attack. Hypnosis also failed and Kingdra was about to knock Noctowl out when the battle was suspended by Team Rocket's antics. Noctowl was not used in the rematch.
Noctowl was used in the battle against Harrison in the quarterfinals of the Silver Conference in Playing with Fire!. It was put at a huge disadvantage by fighting Harrison's Steelix, who blinded Noctowl with Sandstorm and then used Dig to avoid Noctowl's Psychic attacks. A single Iron Tail took Noctowl out of the match.
Ash left Noctowl along with his other Johto Pokémon at Professor Oak's Laboratory when he set off for the Hoenn region.
In Showdown at the Oak Corral, Noctowl was seen on a branch and spotted Cassidy and Butch when they were breaking into Oak's Lab. It appeared later when it was showing Tracey and Bayleef the way to Cassidy and Butch's helicopter.
It appeared in The Right Place and the Right Mime, reuniting with Ash and meeting his Swellow.
Noctowl defeating Lickilicky with Extrasensory
Noctowl reappeared in An Old Family Blend!, alongside Ash's other Pokémon where it was reunited with its Trainer.
In Working on a Right Move!, Ash used Noctowl as his first Pokémon in his battle against Conway in the third round of the Lily of the Valley Conference, where it went up against his Shuckle. Shuckle started off with Withdraw, raising its defense. Noctowl used Sky Attack, and while it was charging, Shuckle used a second Withdraw. Using its Sky Attack, Noctowl then charged against Shuckle who used withdraw a third time, deflecting Noctowl's attack and damaging it. Shuckle then used Power Trick to swap its Attack and Defense, making its attack high but its defense low. Noctowl then used Air Slash, but Shuckle used a powerful Gyro Ball cutting off Sky Attack and dealing major damage to Noctowl. Ash then returned Noctowl. Noctowl was later sent out against Lickilicky, which used Power Whip, but its long tongue was unable to reach Noctowl, who was airborne. Noctowl then dealt damage with Air Slash. After dodging Thunderbolt, Noctowl used Extrasensory, lifting Lickilicky into the air and then dropping it, defeating it. Conway then used his last Pokémon, Dusknoir, Dusknoir immediately used Trick Room, with Noctowl attempted to use Extrasensory. Dusknoir quickly came from behind and used Thunder Punch, knocking Noctowl out before it could use the attack. Conway then explained it was because of Trick Room, as it makes the slowest Pokémon attack first, thus the slow Dusknoir attacking before the normally faster Noctowl.
Noctowl was reunited with Ash in The Dream Continues!, where it and the rest of Ash's Pokémon posed in a group photo with him.
Personality-wise, Noctowl was presented as intelligent, mischievous, and cunning — although these traits weren't usually emphasized or touched upon after its debut episode. It also presents a serious side to its personality, often going to sleep with dignity, or using its hypnosis on others in order to save them, instead of for prank purposes, as was the case in Carrying On!, where it was also shown to develop a soft spot for a small Pidgey. Noctowl is very loyal to Ash because he saved it from Team Rocket, and similar to Bulbasaur, was captured in a fair contest with Pikachu. Noctowl also proved to be a very powerful Pokémon, being used as Ash's secret weapon in his battle with Morty and also performing well in the battle against Conway.