Bunnelby was first mentioned by Clemont in Kalos, Where Dreams and Adventures Begin!, where it was stated to be a recent capture, presumably captured after Clemont and Bonnie were kicked out of the Lumiose City Gym after it was taken over by Clemont's robotic stand-in Clembot. It was used by Clemont to battle Ash's Pikachu. Much to Ash's surprise, Bunnelby was able to dodge Pikachu's attacks with its agility. The two seemed evenly matched, but the battle was interrupted by Team Rocket.
Bunnelby teamed up with Pikachu to try and stop the villains, but Jessie's Wobbuffet deflected Pikachu's attack and almost injured him. After Pikachu was saved by a Froakie, Bunnelby sent the trio into the air with Dig, allowing Pikachu and Froakie to blast them off.
Bunnelby was used in Clemont's Got a Secret! to battle against Clemont's Heliolisk, which was being used by Clembot. Bunnelby was initially overwhelmed by Heliolisk's strong and direct attacks of Bulldoze and Parabolic Charge, but eventually overcame the Generator Pokémon by combining its Dig and Double Team attacks to confuse it.
In Forging Forest Friendships!, Bunnelby was used in a Double Battle with Chespin against Froakie and Hawlucha. Due to an argument between Froakie and Hawlucha, Clemont's Pokémon had the upper hand, but Froakie used its speed to trick Chespin's Pin Missile into hitting Bunnelby, knocking it out. Later, it wanted to eat some of Serena's Poké Puffs, only for Chespin to have already eaten them.
In A Fork in the Road! A Parting of the Ways!, Bunnelby was shown helping Clemont train for his upcoming Gym Battle with Ash, defeating his Magneton in battle and learning a new unknown move.
In The Moment of Lumiose Truth!, Bunnelby was used in Clemont's Gym Battle against Ash, despite the Digging Pokémon not being an Electric-type. It was Clemont's first Pokémon who went up against Pikachu. Pikachu used Thunderbolt, which was blocked by Bunnelby using its ears to create a mud shield. Bunnelby then used Dig, which was too fast for Pikachu to evade. Pikachu followed up with Quick Attack, which Bunnelby quickly recovered from. It then used Double Slap but Pikachu used Iron Tail which the Digging Pokémon caught with its ears. This reminded Bonnie of their first battle. Instead of letting Pikachu counter with Electro Ball, Bunnelby used its new move, Wild Charge, dealing major damage to Pikachu. Bunnelby then hit Pikachu with another Dig. Pikachu responded with Quick Attack, but Bunnelby used Dig again. However, Ash had Pikachu use Iron Tail on the ground, forcing Bunnelby to emerge and dealing major damage. Pikachu then used another Iron Tail, defeating Bunnelby.