Out of all the popular cities in Japan, Sapporo is the cheapest city to rent a car in at just $31/day. Renting a car in Sapporo is 71% cheaper than renting one in Yamagata where the per day rate is around $105. Other fairly inexpensive cities in Japan to get a rental car in are: Okinawa ($33/day), Tokyo ($36/day), and Yakushima ($37/day). While these cities typically have cheaper prices than the rest of the country, travelers looking to rent a car in Tokyo should expect to spend around $36/day on their transportation. The most popular city to rent a car in Japan is Tokyo.