They are keen to organise more regular pet-friendly excursions in the future, Start Up official Shino Furukawa told AFP.
"We've received requests from customers who want to have a relaxing time with their dogs on the train," she said.
"We want to create an environment where people can live in harmony with their pets, who are part of the family. This is a big step towards making pet-friendly public transport a reality."
Japanese trains are famous for being spotlessly clean, and one of the biggest challenges was to maintain the impeccable standards on board, she said.
Staff put plastic covers on all the seats and brought four air purifiers into the carriage, which will be spruced up after the trip to remove all dog hair.
