By ship
By ship

Given that Japan is an island nation, boats are a surprisingly uncommon means of transport, as all the major islands are linked together by bridges and tunnels. While there are some long-distance ferries linking Okinawa and Hokkaido to the mainland, the fares are usually higher than discounted airline tickets and pretty much the sole advantage is that you can take your car with you.

For some smaller islands, however, boats may well be the only practical option. Hovercrafts and jet ferries are fast but expensive, with prices varying between ¥2000-5000 for an hour-long trip. Slow cargo boats are more affordable, a rule of thumb being ¥1000 per hour in second class, but departures are infrequent. There are also some inexpensive and convenient short-distance intercity ferries such as the Aomori-Hakodate ferry.

These boats are typically divided into classes, where second class 2等 nitō is just a giant expanse of tatami mat, first class 1等 ittō gets you a comfy chair in large shared room and only special class 特等 tokutō gets you a private cabin. Vending machines and simple restaurant fare are typically available on board, but on longer trips particularly in second class the primary means of entertainment is alcoholic — this can be fun if you're invited in, but less so if you're trying to sleep.

By road
By road

Japan is an excellent country for hitchhiking, although there is no Japanese custom for this, and some Japanese language ability is almost mandatory. See Hitchhiking in Japan for a more detailed introduction and practical tips for this fine art.

By plane
By plane

Japan's excellent Shinkansen network means that flying is usually more of a luxury than a necessity. That being said, flying remains the most practical mode of reaching Japan's outlying islands, most notably for connections from the mainland to Hokkaido and/or Okinawa. Flying is also useful for getting around sparsely populated Hokkaido, as there is no Shinkansen network there.

Tokyo's Narita Airport handles a few domestic flights, but most domestic flights leave from Haneda HND to the south of the city. Similarly, while there are some domestic flights from Kansai International Airport, more use Itami ITM to the north of Osaka, and Kobe's airport also fields some flights. Narita to Haneda or Kansai to Itami is quite a trek, so allow at least three and preferably four hours to transfer. Chubu, on the other hand, has many domestic flights and was built from the ground up for easy interchange.

List prices for domestic flights are very expensive, but significant discounts are available if purchased in advance. Both of Japan's largest carriers, Japan Airlines JAL, 日本航空 Nihon Kōkū, (http://www.jal.co.jp/en/) and All Nippon Airways ANA, 全日空 Zennikkū, (http://www.ana.co.jp/eng/) offer "Visit Japan" fares where the purchaser of an international return ticket to Japan can fly a number of domestic segments anywhere in the country for only about ¥10,000 plus tax each. These are a particularly good deal for travel to Hokkaido or the remote southern islands of Okinawa. Some blackout periods or other restrictions during peak travel seasons may apply.

The low-cost carrier concept has yet to make significant inroads into Japan, but Air DO (http://www.airdo21.com/index.shtml) provides a little much-needed competition between Tokyo and Hokkaido, while Skymark Airlines (http://www.skymark.co.jp/) and StarFlyer (http://www.starflyer.jp/index.html) serve Tokyo, Osaka and Kyushu. Usually these airlines offer lower walk-up fares than the majors but are not as competitive for advance-purchase discounted tickets.

ANA, JAL, and their subsidiaries offer a special standby card, the Skymate Card, to young passengers up to the age of 22. With the card, passengers can fly standby at half of the full published fare, which is usually less than the equivalent express train fare. The card can be obtained from any JAL or ANA ticket counter with a passport-sized photo and a one-time fee of ¥1000

If you do wish to go on a domestic flight in Japan e.g. Tokyo to Osaka, don't be surprised if a Boeing 747 Jumbo Jet is supplying the short 50 minute flight that you are booked on. Japan is well-known as being the only country in the world to use jumbo jets on short domestic flights of an hour or less, mainly on the Tokyo to Osaka sector.

By Rail

Japan's railways are fast, highly efficient and cover the majority of the country, making this the transport mode of choice for most visitors. The first and most confusing aspect of Japan's railway system especially within large cities like Tokyo that you will encounter is the overlap of several private railway networks with the JR network. Tokyo also has two separate metro systems to add to the confusion. Being aware of this one fact will substantially reduce the confusion you experience trying to understand railway maps and find your way around.

North Americans are usually astounded to find that Japanese trains, like other forms of mass transit, nearly always leave and arrive promptly on time, following the published schedule to the minute. If you are late, you will miss the train!

Note that most trains do not operate 24 hours, for example in Tokyo they do not run between 1:00 AM and 5:00 AM roughly. If you are planning to be out late and are relying on the train to get home, be sure to find out when the last train is leaving. Many bars and clubs are open until the first train runs again in the morning, so keep this in mind as another option.