There are so many car rental companies in Japan. While not many companies don't have English reservation systems, more and more companies offering online English reservations systems these days. But in that case your range of choices is very narrow. There are online English reservation services for foreign tourists that contract with the most of the big companies. And Tabirai is one of them I recommend.

It's very easy to make a reservation from the Tabirai website. You put the date, location, and type of car. Then, you see many choices that matches your request from the cheapest one, so choose the one you like. After that, you can review the details of the car and other add-on options. If you're okay with the conditions, input your name, Email address, and phone number(doesn't have to be Japanese number). That's it. You don't need to sign up or register your credit card information. You'll pay when you arrive at the outlet. You can easily cancel the reservation and send messages if needed through the website.