Building your travel itinerary

Public transport works fine in Japan. It is fast, clean, safe and (in my opinion) cheap for what you get. And they take you everywhere.

Here, the best website for building your travel itinerary within Japan: just provide departure and arrival station, and eventually other minor data, and you will have it.

JORUDAN

Shinkansen (bullet train->Route,schedules and fees), links the mayor cities in the main island. It is probably the best option if you are hoping around Tokyo/Osaka/Kobe/Hiroshima (mayor tourist places).

However, unless you have the JR pass, the shinkansen may be out of budget. For this reason, you may be also interest in night buses. They are cheap (one third of the train price), clean and safe. I tried them and it is a very suitable alternative honestly.

This is the company that I usually use: clean, friendly and 100% time keepers: 123bus.jp