Shinkansen (Bullet trains) and most Limited Express and Ordinary Express trains have reserved Green Car seats (First class) and both reserved and non-reserved Ordinary Car seats (Standard class).
For a non-reserved seat, simply show your Japan Rail Pass to board.
To make a seat reservation, visit any Travel Service Centre or reserved-seat ticket office called “Midori-no-madoguchi” at a Japan Railways station in Japan.
Normally, seat reservations cannot be made from outside Japan. For users of the Japan Rail Pass, seat reservations are free of charge BUT you cannot reserve seats until you have presented the Exchange Order in Japan and obtained the actual Rail Pass.
However, JR East now have an online seat reservation system. This allows travellers to make advance seat reservations for all JR East Shinkansen (Bullet trains) as well as certain JR East Limited Express trains.
This system allows JR Pass holders, JR East Pass holders and also non-pass holders to make seat reservations.
To make a reservation, travellers have to enroll as a member (sign-up is free). Then check the types of trains and specific times, and reserve seats. Travellers just need to pick up the tickets when they arrive in Japan (at any location specified by East Japan Railway Company within the JR East area).
JR East Shinkansen Reservation website
JR Shinkansen Notice: From mid-May 2020, when bringing baggage of total dimensions between 160 cm and 250 cm into the Tokaido/Sanyo/Kyushu Shinkansen (Tokyo – Nagoya – Kyoto – Shin-Osaka – Hiroshima – Hakata – Kagoshima-Chuo), passengers will be required to make an advance reservation for a seat with oversized baggage area (free of charge, limited availability). If no prior reservation has been made for those specific seats, the passengers will be required to pay a 1,000JPY fee per piece of luggage and also to move it to a space designated by the conductor.
We recommend sending your large baggage to your next destination with a specialised courier service. Luggage Free Travel offer a luggage transfer service that delivers items from one Japan destination to another in 24-48 hours (timing dependent on location). Please enquire for more information here.