Palpitoad debuted in Facing Fear with Eyes Wide Open!, where he was the leader of a group of wild Tympole that lived in a lake. Ash and Oshawott had unknowingly invaded his territory while looking for an underwater plant to help his, Cilan's, and Iris's Pokémon heal after being poisoned by wild Foongus that were disturbed by Ash's Scraggy. Palpitoad was angered by their intrusion, and ordered his Tympole cohorts to attack them. When they swam away in fear of Oshawott, he called upon his friend, Stunfisk's, help. However, when Cilan fished Stunfisk out of the water, Palpitoad was forced to face Oshawott himself. Despite knowing some powerful moves, the Vibration Pokémon lost to Oshawott's newly mastered Aqua Jet, and was caught by Ash.
In Reunion Battles In Nimbasa!, he was used in the Club Battle Tournament against Burgundy's Stoutland. Despite being his first battle with Ash as his Trainer, the two synchronized well, avoiding Stoutland's attacks and dealing out powerful blows. Eventually, Palpitoad was caught in Stoutland's mouth when it used Thunder Fang, though he avoided damage from the Electric-type move, being part Ground-type. However, Burgundy took the chance, and ordered an Ice Fang attack, which became a problem for Palpitoad until he used Supersonic to shatter the ice, and knock Stoutland back. After blocking Stoutland's Fire Fang with Mud Shot, Palpitoad won the match with a direct hit from Hydro Pump. In Club Battle Finale: A Hero's Outcome!, Palpitoad battled Dino's Darumaka in the semifinals and won with a single Hydro Pump, allowing Ash to move on to the finals.
In Dazzling the Nimbasa Gym!, Palpitoad was used in Ash's Gym battle against Elesa. Being immune to Electric-type moves, Palpitoad was the ideal choice for this battle, and was Ash's sole strategy for the battle. Palpitoad took many ineffective hits from Zebstrika's Flame Charge and a Double Kick attack, proving unable to dodge. As Zebstrika headed towards Palpitoad using Quick Attack, Ash commanded a Supersonic attack, which blocked and confused Zebstrika. Palpitoad then finished the match with a Mud Shot, followed by a Hydro Pump. Palpitoad showed signs of fatigue after Elesa recalled Zebstrika, so both Iris and Cilan suggested that Ash should recall him and switch to another Pokémon. Ash, however, decided to stick with Palpitoad when Elesa brought out Emolga. However, Palpitoad found himself unable to keep up with Emolga's fast moves, and was hit by an Acrobatics attack, and several Aerial Ace attacks before he was hit with Emolga's Attract, causing him to become immobilized by infatuation. After another couple more hits from Aerial Ace, Palpitoad was knocked out, ruining Ash's strategy for the battle, but Ash later regained his composure and won.
In Rocking the Virbank Gym! Part 2, Ash used Palpitoad as his fifth Pokémon during his Gym battle against Roxie and her final and strongest Pokémon, Garbodor. Palpitoad first tried to use Mud Shot on the Trash Heap Pokémon, but Garbodor used its extendable arms to raise itself from the floor and dodge the attack. As Garbodor attacked with Hyper Beam, Palpitoad used Hydro Pump to block it. Palpitoad then tried another Mud Shot, but it was blocked and countered by a Gunk Shot attack, which poisoned Palpitoad as it hit. Garbodor attacked Palpitoad two times with Venoshock, being twice as powerful because of the poison, and he was knocked out.
In Strong Strategy Steals the Show!, Ash used Palpitoad in his Vertress Conference battle against Stephan and his Zebstrika. At the beginning of the battle Zebstrika was too fast for Palpitoad and avoided its Mud Shot before striking back with Double-Edge and Stomp. However, Palpitoad was shown to have learned a new move, Sludge Wave, which caused Zebstrika to become poisoned when the attack hit. Despite this, Zebstrika was able to fight back, even using the poison as an advantage when using Facade, which did a lot of damage to Palpitoad. Ultimately Palpitoad managed to hit Zebstrika with Supersonic, causing it to damage itself due to confusion. Palpitoad then managed to launch a hit with Hydro Pump. Stephan in turn ordered a Giga Impact which sent Palpitoad flying. However, Palpitoad managed to fire a Mud Shot while in the air just before crashing into a wall, fainting. The match ended with a tie as Zebstrika fainted at the same time from the Mud Shot Palpitoad managed to execute.
In Farewell, Unova! Setting Sail for New Adventures!, Professor Juniper sent Palpitoad to Professor Oak's Laboratory before Ash left for Kanto, touring through the Decolore Islands. He later reunited with Ash and the entire Unova team at Oak's lab in The Dream Continues!. Palpitoad joined in with them to launch a group attack on Team Rocket, using Mud Shot to send them blasting off for the final time in Pokémon the Series: Black & White. Palpitoad later posed in a group photo with the rest of Ash's Pokémon. Then, he was left at the lab when Ash set off for the Kalos region.