Getting around while in Japan. *Would not recommend driving while in Japan if you are just visiting.
Railways
One key way to get around Japan is by using the train system. The #1 app to use when traveling by train is Hyperdia. Also get a Sucia card for the trains.
Airplanes
Air travel is one way to get to the smaller islands of Japan. Also, if you are traveling to Japan from another country you might want to try to fly into the smaller airport of Haneda instead of Narita.
Buses
There are two different types of bus transportation: short distance (inner city buses), and long distance buses. Note: If you are wanting to use a bus for long distance travel a bus pass will come in handy.