Medarot 3 was released in 2000 for the Game Boy Color. It was released in two versions: Kabuto and Kuwagata.

The game follows Ikki Tenryou and his friends in the town of Omikuji. After Ikki robottles with the Screws, everyone's Medarotch data is suddenly deleted by an unknown figure.

Medarot 3 introduced various new gameplay aspects, including Medachange and Medalias.