If you are going to use a “Green” pass, you will need to make seat reservations, as Green carriages do not have unreserved seats.
If you are going to use an “Ordinary” pass, you can choose to reserve seats on specific trains, or just take “unreserved” seats. It is particularly advisable to get seat reservations during busy times, eg. 28 December – 6 January, 27 April – 6 May (“Golden Week”), and 11-20 August (Obon season).
Japan Rail Pass itself does not insure seating options. If you want to use reserved seating, be sure to get seat reservations before boarding (no additional payment needed).
To obtain a reserved-seat ticket, present Japan Rail Pass at the ticket office (Midori-no-madoguchi) at a JR station, a Travel Service Center. When using some trains, you are required to receive a reserved seat ticket, too.
You can use non-reserved seating with Japan Rail Pass alone. Please note, however, that some trains do not have non-reserved seating. Also, if you wish to travel in a private compartment on a Shinkansen or a limited express train, you will be required to pay the limited express charge for the private compartment, as well as the Green Car charge if the private compartment is a Green Car accommodation.
An extra charge is also required if you wish to travel in a sleeping car, a DX Green Car or Gran Class accommodation. If you ride in a Green Car using an ordinary car pass, you will be required to pay the Green Car charge, as well as the limited or regular express service charge. (No extra charge applies when using a Green Car pass.) You must also pay an extra charge in advance to travel on a local train requiring a numbered ticket or a liner ticket. Japan Rail Pass does not allow you to change to a reserved seat or sleeping car after boarding.
If you use non-reserved seating, or if you travel in an ordinary car using a Green Car pass, no refund shall be paid for the fare or other charges.