The Johto region is the second region to be explored, located to the west side of Kanto. Johto and Kanto are part of one large continent, with everything to the west of the Indigo Plateau considered part of Johto. Because of the close proximity of these two regions, they both share the same location for the Pokémon League. Johto is also the tiniest region, but Nintendo made up for it by including Kanto in the same game, but Kanto was also smaller for some reason.

This region was first revealed in Gold/Silver/Crystal, along with 100 previously unknown Pokémon. In the Generation II games, the player's home town is New Bark Town, where they can choose either Chikorita, Cyndaquil, or Totodile as their first Pokémon.