30 useful tips for travel in Japan

Booking Tickets for Trains and Buses
Transportation
If you're not going to be using the Japan Rail Pass, you'll need to buy your express train tickets from the departing station. There are machines to buy tickets for JR bullet trains, with guidance in other languages as well, but you may want to purchase it from the teller just to make sure everything is in order.
JR Express Trains
The main thing to take note of when buying bullet train tickets is the distinction of "free-seating " versus "reserved seating”. Free seating is generally the front or rear three cars of the“Nozomi” bullet train. Outside of peak travel times, it is rare for the reserved seating to fill up, although there is still a chance you could be left without a seat, Like regular trains, bullet trains can still be ridden on the non-reserved seat car even if every seat is taken. Reserved seating is offered and designated at the time you buy your ticket. If you are traveling in a group and want to sit together, this is the safe option. You can choose whether you would like free or reserved seating at the time you purchase your ticket. Purchase tickets from a teller or machine at the "Midori no Madoguchi" ticket office in major stations.
Other Express Trains
There are many other train companies besides JR, and they offer express lines just the same. While they are technically not "bullet trains", there are many options for high speed train travel outside the JR areas by the railway operators such as Odakyu, Tobu and Kintetsu. For example, Odakyu Electric Railway offers express services to popular areas such as Izu and Hakone from Shinjuku. Tickets are secured in the same way; reserve at Odakyu line stations, or travel agencies.
As JR express trains only pass through the most densely populated areas of Japan, you will find that it is necessary to branch out to other lines in some cases. The ticket buying process is very streamlined at major stations, and employees are extremely helpful.
Expressway Buses
In most cities in Japan the highway bus stations will be located at or very near the central railway station, which also makes them convenient to use. For example, in Tokyo the new Basuta Terminal is located near the JR Shinjuku station. All tickets can be purchased at any of the ticket windows there. It's a major highway bus facility, and you will likely find yourself there if you're departing Tokyo on a bus.

However, beware that many bus stops on the highway can be in relatively remote areas and not in the center of towns – so you may need to research carefully to make sure where you get off is near your destination or you can get transport from the bus stop to where you need to go.

However, many bus lines do run seasonal direct routes to out of the way places. For example, the quickest and easiest way to go from Tokyo to Kamikochi, a popular summer hiking mecca, is by highway bus and many ski resorts are serviced by direct bus services from the cities.

There are hundreds of highway bus companies but the main ones are run by the railway companies.