The 1993 film Teenage Mutant Ninja Turtles III features time travel to feudal Japan. The 1993 The Legend of Koji episode of the 1987 Teenage Mutant Ninja Turtles TV series also features time travel to feudal Japan.
In the 2003 animated series, Japan played a more important role during the series fifth season. It was the homebase of the Ninja Tribunal, where they had a palace called The Lap of the Gods. They had recruited the Turtles and 4 other, human fighters to train there and combat a reincarnation of the Tengu Shredder.