Especially for all-reserved trains, but also for others, one sometimes needs or wants to reserve a seat on a JR train, even with a rail pass. When and how can one do so?
As a general rule, reservations for a given train open at 10am (Japanese time) one month before departure. For example, reservations for a train departing on May 20 open at 10am on April 20. Reservations close when the train departs. Some things to note:
- If there is no "matching day" in the previous month, reservations open on the first day of the month of departure. For example, reservations for a train departing on May 31 open on May 1.
- During busy travel periods, reservations may open earlier than normal. There is no set rule for when or how this happens (it is announced in various ways, such as on JR websites and on posters in stations).
- For trains operating after midnight, the departure day is the day on which the train leaves its departure station. However, if you board the train after midnight, you must make a reservation for the day when you board. For example, reservations for the Sunrise Izumo leaving Izumoshi for Tokyo at 18:57 on May 20 open on April 20. However, if I board this train in Osaka at 00:32, I must make a reservation for May 21 (but I can make this reservation on April 20).
- Just like some trains are all-reserved, some others are all-non-reserved, and thus do not allow reservations (at least for ordinary class seats; they may have some reserved Green class ones). This is mostly the case for ordinary commuter trains, but also for some express trains such as Nasuno trains on the Tohoku Shinkansen between Tokyo and Koriyama. As mentioned at the bottom of this answer, Hyperdia can be used to check the available seating options on a particular train.
At ticket offices
For most trains, this is the only way to make a reservation with a rail pass.
The most common way to reserve a seat, especially for foreign travelers, is at ticket offices such as the Midori-no-madoguchi (みどりの窓口, lit. "green window") which can be found at most JR stations in Japan. (Only the smallest stations, usually in rural areas, do not have one.) It is not necessary to make the reservation at the departure station of the train; there is usually a long wait line at the ticket offices in major stations, so doing it at a smaller one usually results in shorter waiting times. The business hours of the Midori-no-madoguchi at a given station (if there is one) can be found on its station information (駅情報) page on the operating company's website, which can be found by just typing the station name in Japanese (with the suffix 駅) into a search engine. For example the one at Aobadori station (あおば通駅) is open from 7:00 to 21:00.
The necessary information to make a reservation are the departure and arrival stations, and the date and time of departure. Also mention any specific request such as specific seats, and present your rail pass if you have one. For easier communication if you do not speak Japanese, you can just write the information on a piece of paper beforehand, or take a Hyperdia screenshot on your phone.
Payment (if necessary) is by cash or credit card. Foreign cards are normally accepted. If paying by card, you will be asked for your signature (not your PIN).
At ticket machines
Ticket machines can also be used with screen text in English, but their usage can be confusing if one is not familiar with the Japanese rail system, and they do not work with rail passes. Payment is again by cash or credit card (if paying by card, you will be asked for your PIN). On machines displaying the IC logo, payment can also be made using the balance on a Suica or compatible IC card.
Online in English
JR East's service is the only rail-pass-friendly one, but it only allows reservations for travel within the JR East (in yellow/green) and JR Hokkaido areas. In addition, tickets must be picked up at a JR East or JR Hokkaido station by 9pm the day before departure, and so it is not possible to reserve seats for trips on the day of arrival in Japan. Although the English website is part of the eki-net system mentioned below, tokudane discount tickets cannot be purchased from it. Consult the website for the (many) other restrictions, especially regarding the times when reservations can be made. If you are not using a rail pass, payment is by credit card only. A simple registration process is also required.
JR Central's service works through a smartphone app, which is as of this writing only available in some countries in the Asia-Pacific region and in the United States, rather than a website. It only allows reservations on the Tokaido and Sanyo Shinkansen (between Tokyo and Hakata, including Nagoya, Osaka, Kyoto, or Hiroshima), and it does not work with rail passes. On the other hand, it does give access to some of the discount tickets previously only available on the Japanese portal, and it also allows ticketless travel by loading a reservation onto a Suica or other compatible IC card and using it to pass through the ticket gates. Either way, payment is by credit card only (even if using an IC card, it is not possible to pay with the balance on the card).
Online in Japanese
Each JR company operates an online reservation portal in Japanese, where reservations can be made for virtually all JR trains in Japan, and must be picked up at a station of the company operating the portal, either at a ticket counter or at ticket machines. The different portals are well described in this answer.
Some portals offer Internet-only discounts, for example JR East's portal eki-net offers トクだ値 (tokudane) fares for JR East trains, with up to 35% discounts over regular fares (applicable discount rates differ by route). The best discounts are obtained by booking up to 13 days before departure, but discount tickets are limited and sell out quickly on popular routes (such as between Tokyo and Sendai). eki-net also offers an advance reservation service, whereby tickets can be "pre-reserved" from up to a month before reservations formally open. (Seats are then allocated on a first-come, first-served basis when reservations open.)
Registration is also required, and is more involved than on the English websites; in particular a Japanese address and phone number are required (for tourists, your hotel's information will do). While those services are of course not officially aimed at rail pass users, some people have reported that they successfully booked tickets on them and had the fees waived when they presented their rail pass when picking them up–try this at your own risk.
One additional tip I discovered:
I found that when I went to reserve seats (speaking to the staff in English) they could sometimes be confused by the service numbers. So instead of saying that you'd like to reserve seats on the "Hikari 54" (for example), it is probably safer to say you'd like to reserve the "13:45 Hikari", using 24 hour time. I have no idea if people would normally refer to services by their numbers or their times in Japanese, but I had more success in English doing this.