Empoleon was first seen as a Prinplup in Getting the Pre-Contest Titters!. It proved to be very strong when it battled Ash's Pikachu despite Pikachu having the type disadvantage. In the next episode, it put up a good fight against Dawn's Piplup. At first, Prinplup didn't want to be friends with its weaker, pre-evolved form, but after being saved by Piplup, they soon became friends.
Prinplup appeared in a flashback in Buizel Your Way Out Of This!. It then made a cameo appearance in Throwing the Track Switch during Marian's television show, in which it was revealed to have helped Kenny win the Sage Town Pokémon Contest, earning Kenny his second Ribbon.
Prinplup briefly appeared in the beginning of Journey to the Unown! with Kenny. In Team Shocker!, Prinplup helped Kenny get to the final round of the Solaceon Town Contest, but eventually lost to Jessie's Dustox.
Prinplup made a cameo with Kenny on television in A Breed Stampede!, where it was revealed to have helped him earned his third Ribbon.
In Stopped in the Name of Love!, Prinplup appeared alongside Barry's Empoleon and Dawn's Piplup. As it tried to help search for Piplup, who had run away while trying to resist evolution, Prinplup and Barry's Empoleon were kidnapped by Team Rocket's Piprinoleon robot. Prinplup was recovered through Dawn and Piplup's teamwork.
In Old Rivals, New Tricks!, Prinplup was used in the Battle Stage of the Sandalstraw Contest. It managed to defeat its first two opponents to reach the finals, where it went up against Dawn's Ambipom. Prinplup started the battle by using Drill Peck, but Ambipom blocked the attack with Swift and then used Double Team. After that, Prinplup used Bubble Beam to destroy the illusory copies Ambipom had created. However, before the attack could hit the real Ambipom, Dawn had the idea to implement ping pong moves into the battle and asked Ambipom to use Focus Punch, sending the bubbles back to Prinplup.
Seeing that, Kenny asked Prinplup to repel the bubbles with Metal Claw. The bubbles went back and forth for a while until Prinplup used Bubble Beam again. This time, instead of repelling the bubbles, Ambipom used Double Hit to destroy them. With the bubbles keeping Ambipom busy, Prinplup approached her with Drill Peck, but Ambipom saw Prinplup coming and countered with Focus Punch. The two clashed in midair but Prinplup quickly recovered, jumping high and then using Drill Peck while nosediving and spinning. Ambipom proceeded to use Double Hit, but the move was unable to stop Prinplup. Ambipom was taken aback by this and Prinplup attacked her with another Drill Peck, knocking her out and winning the battle. This victory gave Kenny the Sandalstraw Ribbon, his fourth Contest Ribbon overall.
Between helping Kenny win the Sandalstraw Ribbon and Kenny's participation in the Grand Festival, Prinplup evolved into Empoleon and learned two new moves: Flash Cannon and Hydro Cannon.
In Last Call — First Round!, Kenny used Empoleon alongside his Floatzel in the Performance Stage of the Sinnoh Grand Festival. However during an attempt to create a Flash Cannon-Whirlpool combination, Empoleon accidentally knocked Floatzel out, its Flash Cannon being too powerful for Floatzel to handle. As a result of this mistake, Kenny failed to make it past the first round.
In Four Roads Diverged in a Pokémon Port!, Kenny used Empoleon in a battle against Ash's Buizel, in which it was able to defeat Buizel. It also seemed to have developed a rivalry with Buizel following its win.