JR East will launch the service in July, with one carriage on the "shinkansen" bullet train having two 2.4-metre-long tubs facing windows.
Bathing is a ritualised and highly-prized activity in Japan and the footbaths are intended as places for passengers to relax rather than to clean their feet.
The train, named Toreiyu - a rather tortured combination of the English "train", the French "soleil" and "yu", the Japanese word for hot water - will also have a car with a bar counter and tatami-mat flooring with tables made from cherrywood.
The train will run on a 148-kilometre route between Fukushima and Shinjo City in Yamagata prefecture mostly on weekends. It is part of a campaign to promote tourism in Yamagata, a farming area known for rice, beef, cherries and pears.
The inland city of Fukushima is more than 60 kilometres northwest of the tsunami-crippled nuclear power plant on the Pacific coast.