*Last updated Nov 10th, 2023
Intercity travel can be quite expensive in Japan.
Using the extensive network of bullet trains (Shinkansen) is the easiest and fastest way to travel, as services are frequent and don't require a check-in process like airplanes. However, the costs are not small - a one-way ticket from Tokyo to Osaka will cost a little under 15,000 yen.
Use of airplanes could be suitable for destinations further away. The locals generally prefer trains if the travel time is under four hours. This includes destinations such as Osaka or Kanazawa. For Okayama (with the connection to the art museums in Naoshima), it's a close call and some travelers prefer flying.
If you are going further such as Hiroshima and Fukuoka, taking a flight will save you much more time and depending on the timing of reservation, it may also be the cheaper option to taking the Shinkansen.
The era of the low-cost carriers began very recently in Japan; Peach Aviation began flying in 2012. All domestic LCC flights use Narita as their base (not the more convenient Haneda) and are known for delays and even cancellations as they try to operate with the minimum amount of fleet - they are no different from the LCC's seen elsewhere in the world.
Jetstar has many destinations in Shikoku and Kyushu in addition to Sapporo and Okinawa. Peach Aviation has flights mainly out of Osaka's Kansai Airport though a number of routes also exist from Narita to cities in Kyushu and also Sapporo.
Both of these airlines have very early morning departures from Narita that leave between 7-7:30am. If booking these flights, do double-check before booking if you can make it to the final check-in time, as you will likely have to catch one of the first trains of the day from central Tokyo (Trains in Japan do not run 24 hours).
If your flight is scheduled to arrive in Narita after 10pm, also check in advance the last trains heading to your final destination. Narita has a curfew (23;00) so a major delay could cause cancellations. Do have a backup plan if bad weather is foreseen which may cause a delay.
While most of their flights are on the expensive side, do also check the full service carriers such as ANA and JAL. They occasionally have bargains especially when booking several months in advance. ANA and JAL uses the more convenient Haneda Airport which is a huge plus.
"Highway Buses" can be a much cheaper alternative to the trains and flights. It's highly unlikely that the driver will speak English, and usually reservations are necessary - you cannot simply hop on the bus, at least for those traveling long distances. There are probably hundreds of various-sized operators with varying degree of service levels.
JR is known for the Shinkansen but they also operate a super-express bus that connects Tokyo Station with Nagoya in five hours. It might be more than three times the duration of a Shinkansen ride, but the fare can be as low as 3,000 yen if you are travelling on a weekday with advance reservations. However they lack any English reservation site, so you might have to show up at the ticket office on the Yaesu south side of Tokyo station to claim your tickets in advance.
Willer Travel runs services to all parts of Japan (including some that run during the night, which would save some accommodation costs too) mostly from new bus terminal "Busta" adjacent to Shinjuku Station. You might be able to find a deal to Kyoto or Osaka for around 4,000 yen, if you can endure 8-9 hours in a cramped space. The overnight buses have compartments for luggage, and the drivers will be courteous in helping with the storage.
All buses will make a 15-20 minute stop at a parking area every 2 hours, as a regular break for drivers is now mandatory under the new safety guidelines. Most drivers will set up a board with the departure time written down, so non-Japanese speakers can also understand when the buses will leave. Buses will not wait for late passengers so make sure you return to the bus with sufficient time.
The major operators generally have no safety issues, but smaller companies seem to sometimes sacrifice their safety standards to allow for lower rates. Non-Japanese readers probably won't bump into them anyways as they rarely have any English websites, but it is advisable to stick with the bigger companies such as JR or Willer.
In recent years, many bus companies are struggling to hire enough bus drivers to keep up with demand. This has resulted in services being cut even in some of the profitable routes. Always verify through official online sources for the most updated schedule. This trend is expected to worsen as working population continues to shrink in the country.
Where the buses depart from:
Most of the long-distance buses depart from either the new terminal in Shinjuku or on the Yaesu side of Tokyo Station. However the location can vary depending on the operator, so it is always important to check in advance!
The terminal opened in 2016 next to the south exit of the Shinjuku Station. There is a waiting area, a convenience store and restrooms in the departure area on the fourth floor. This is where many of the services headed to Lake Kawaguchi, Matsumoto and Takayama depart from. There are also frequent departures for both Haneda and Narita Airport. There is a counter with English-speaking staff in case you need assistance with getting tickets or figuring out where your bus will be leaving.
Previously, bus departures from Shinjuku were scattered throughout different areas of the station but they have all been consolidated here. Old publications may still mention the existence of a Keio or Willer terminal on the west side of Shinjuku but this has closed down.
TOKYO STATION, YAESU SIDE
Many of the JR-operated buses depart from the terminal just outside the Yaesu Exit on the eastern side of Tokyo Station. This is where buses for Shizuoka and Nagoya depart from, and there are also services to both Hakone and Lake Kawaguchi from here as well. There is a ticket counter and also automated ticket machines in case you haven't made a reservation yet. The waiting room is small but you can also use the facilities of Tokyo Station which is almost like a huge shopping mall.
KAJIBASHI TERMINAL, TOKYO YAESU SOUTH
Many of the smaller operators use the Kajibashi Terminal which is about 5 minute walk south of Tokyo Station. There is very little space to wait for the buses and for non-Japanese speakers it may be a challenge to determine where your bus is leaving from, as there are multiple berths with buses continuously going in and out.
Overnight Trains hardly exist anymore...
The country used to have a very extensive network of overnight trains, but now only one regular service remains.
The Sunrise Express runs between Tokyo and Izumo-shi/Takamatsu everyday. The trains split at Okayama, with half the trains going to the Sea of Japan side, while the other crosses the Seto Bridge for Takamatsu, Shikoku Island's largest city.
There are private rooms for one or two people and showers available, but the trains do not have a dining car.
Like other trains, reservations open exactly a month in advance, at 10am Japan time. They remain a popular way to travel and tickets often sell out quickly.
Tokyo used to have multiple ferry links to Hokkaido and Shikoku, but now only one remain. Ocean Tokyu Ferry operates a daily service leaving the Tokyo Ferry Terminal (South of the Tokyo Big Site convention hall, no public transportation) at 7:30pm Monday-Saturday or 6pm on Sundays and arriving the following afternoon in Tokushima, Shikoku. The ships are all new and really comfortable, but does not come with a restaurant. You either bring food into the ship yourself or buy it onboard from the vending machines!
The direct link to Hokkaido has been discontinued for quite some time, so you will have to travel to the Port of Oarai which is at least 2.5 hours from central Tokyo. From there, MOL Sunflower operates two services a day that will take a grand total of 19 hours to the Port of Tomakomai. From there, it is roughly an hour to Sapporo by connecting bus service. With plane tickets that are available from 5,000 yen, choosing to travel via the sea is no longer a cost-saving solution.