As you travel around Japan keep in mind that certain times of year are easier than others, and it is best to avoid busy periods around major holidays. These include New Year, late April and early May, and the Obon holiday in the middle of August. At these times tickets are usually booked well in advance and are more expensive than usual.
Japan has a fantastic rail system that includes both the ordinary rail service and the high speed bullet train the shinkansen. The railway network in Japan runs all over the country and is convenient, clean, and efficient, although it is not particularly cheap if you buy single tickets. If you want to cut costs then buying a rail pass that will give you discounts is the best choice. Unfortunately these passes don’t apply to the shinkansen, and unless you are really in a hurry or just want to say that you have been on one then there is not much reason to choose this over one of the regular trains. It’s easy to buy train tickets at stations in Japan and contrary to popular belief the names of the stations are also in English so that you will know where you are going and when to get off.
If you want to travel further distances then it may make more sense to fly. Luckily Japan has several domestic airlines in the form of All Nippon Airways, Japan Airlines, Skymark, Air Do, Skynet Asia Airways, IBEX Airlines, and Starflyer although some of these only travel certain routes and don’t fly all over the country. Due to the fact that there is a lot of competition, many airlines offer fantastic discounts on tickets, especially if you book online and it can often work out cheaper than taking a train so shop around first to make sure that you get the best deal.
For even cheaper travel around Japan you might want to consider taking a bus, many of which have cheaper rates than the trains and are safe and convenient, although you might get caught in traffic which will make the journey longer. You can also buy a ticket on the bus instead of having to book ahead which can be convenient in many scenarios.
Less used by travelers, unfortunately, are the ferries which travel to Japan’s many islands. Many of these run overnight and have cheap fares and are in good condition with high safety standards. Be aware that usually you will not get a cabin for yourself. Instead you’ll mostly be sleeping on the floor together with other passengers, so this is only an option if you feel comfortable with this. That said, some routes will allow you to pay extra for your own cabin and this is usually quite cheap. If you get the chance then this is one of the nicer ways of travelling around Japan.