Riding the bullet train is a great way to get around the country; often times much faster than going to the airport and having to go through all the security. There is no check-in process for riding the trains, so you just go the station and find the platform where your train is leaving.
This section gives you some advice on using the bullet trains, known as the "Shinkansen"
Q: Do you need seat reservations?
A: Some trains like the Kagayaki that goes to Kanazawa, or the Hayabusa train that goes to Hakodate, Hokkaido require a seat assignment prior to boarding. The New Year Holidays, the Golden Week Holiday period in May, and the O-bon period in mid-August is when trains tend to get full. Reservations open a month before.
At other times, there usually isn't too big of a concern about all the seats selling out. If you are traveling along the main route between Tokyo and Kyoto/Shin-Osaka, services are so frequent to the point where there are departures every 10 minutes during the peak hours. Most locals just get a ticket from the automated ticket machines (English option available) when they arrive at the station. While the machines accept credit cards, I have noticed that international credit cards get rejected at a very high rate. In that case, you'll have to line up at the ticket office which can take a few minutes. Like in many other places in Japan, it probably is a good idea to be carrying around some cash with you.
Most trains have a few cars which are designated as non-reserved. You simply find a open seat after you get on the train. On the Nozomi trains, this is car 1, 2 and 3. If you are heading to Kyoto, chances are very slim that any of the non-reserved seats will still be vacant when the train arrives at Shinagawa or Shin-Yokohama, so make sure to get a seat assignment before boarding. If your departure point is Tokyo, you have more chances of finding seats for the non-reserved cars.
For the slower Kodama series train, almost the entire train is designated as non-reserved cars. Unless you are traveling in a big group, there is really no need in getting seat assignments as there will always be a seat available somewhere.
The reserved seat cars are for the use of passengers with advance seat assignments. Even when there are open seats, you are not allowed to sit in them if you don't have reservations.
Q: Are there any online booking available?
A: JR is broken down into six different companies and there is no universal ticketing site where all the trains can be booked.
JR East has their online platform for its northbound trains (Destination Niigata, Sendai, Yamagata, Akita and Shin-Aomori) and also on the Hokuriku Shinkansen (Nagano, Toyama and Kanazawa) which it runs in conjunction with JR West.
For the Tokaido/Sanyo Shinkansen (the main route that runs between Tokyo-Kyoto-Shin Osaka-Hiroshima) go to the Smart EX website which is run by JR Central. These trains run very frequently, so most of the time you can visit the ticket office or automated ticket machine moments before you travel and have no problems in getting the tickets you need.
Q: Can luggage be brought on-board?
A: There is space above the seats to put suitcases or backpacks and it will fit most sizes. If you have oversized (or heavy) suitcases that cannot go on this space, one possible solution is to try to make use of the space behind the final row of the train. Always ask for permission from the person sitting on the last row, as putting luggage may obstruct the passenger from reclining the seat. (See below- for certain trains it is no longer possible to do this from May 2020)
Most of the northbound trains run by JR East have luggage space at either ends of the car and with the increase of international tourists, there are plans to install more in the coming future. For now, it is advised to be travelling light; otherwise make use of the Takuhaibin (luggage forwarding service) that many hotels can arrange for a fee in order to avoid bringing in large objects to the trains.
Changes effective May 2020
The Shinkansen trains running on the main Tokaido route (Nozomi/Hikari/Kodama/Mizuho/Sakura) are putting tighter restrictions on what can be brought onboard.
Any baggage with overall dimensions of over 160 cm (62 in) will need to be placed at the designated space behind the rear row of each car.
There is no additional fee for reserving the luggage space if arrangements are made at the ticket office in advance, but a 1,000 JPY fee will be charged from the conductor if travelers show up on the train without one.
For the JR East operated trains (including the Narita Express train and services to Hokkaido and Kanazawa) there is no need for booking space in advance as they have extra luggage space. The same for the Haruka Express train linking Kansai Airport with Osaka and Kyoto.
Q: What are the facilities on-board the train?
A: All seats have a tray and a pocket to put drinks and belongings. Many of the newer trains have power sockets (100V) on the window-side seats for recharging mobile phones. Some the older trains used in the Hikari or Kodama service between Shin-Osaka and Hakata only have sockets at the very front and back of each car.
Most trains have free WIFI but it is unstable in mountainous areas. Also with a full train, getting a good connection could be more difficult.
It is ok to eat and drink in your seat. It is advised to make a purchase before boarding as services onboard the train are discontinued on many trains due to staff shortages.
There is a toilet in either end of each car.
All seats are now designated as non-smoking.
The Nozomi/Hikari/Kodama trains have a small smoking room located at the end of cars 3, 15 (for normal seat passengers) and car 10 (for Green Car users)