I live in the middle of nowhere in Japan, and have toured all but 7 prefectures. I love travelling the countryside, but a decade ago I couldn't speak the language and it could get anxiety-inducing. Here's some tips I wish I'd known then.

Frequency

This one is a given, but bus and trains in the countryside can be VERY infrequent (we're talking hours between each time slot), even moreso during major holidays. Do your research before planning out a day.

Navigation

All the typical apps (Google Maps, Apple Maps, etc) are pretty reliable and up to date with the timetables for either bus or train. For bus, just be prepared to have your bus unexpectedly skip a stop because of road closures and the like.

For peace of mind, I prefer to always take a picture of the physical timetable attached to stations/bus stops. They will ALWAYS have the latest information with 100% certainty.

Ticket types

1. IC: not always possible in the countryside. Whether it's JR or a local rail/bus company, there are many lines where IC cards are not accepted for the entire length, or sections of the line.
   1. This information is usually posted at major stations prior, but you can check in advance. Google the name of the station you want to get off, and see if it has a gate for an IC-card.
2. Ekinet QR code: Via ekinet app (typically inaccessible to non-residents), scan it at the QR reader at the gate. Same restrictions as IC cards
3. Physical tickets
4. Numbered ticket (整理券 aka Seiriken)
5. Boarding voucher: A stamped voucher declaring your station of origin
6. Day pass:: Allows you to freely board the bus/train on the date(s) stamped on the pass. Show it to the driver/conductor when you board or disembark, or to the station staff.

Train

Paying for your ticket

1. Unmanned station: many stations in the countryside are unmanned. There likely isn't even a ticket machine. If you're boarding from an unmanned station and disembarking at an unmanned station, that means that you will pay on the train. If you're boarding from an unmanned station and disembarking at an manned station, you will pay either on the train or at the terminus station window.
   1. Paper ticket: Sometimes the conductor themselves will come to you. Tell them the name of your destination station, and you can buy your ticket then and there. Ideally, have the exact money prepared in advance, fumbling around for change adds stress to the conductor who has a schedule to keep. When you disembark, you hand over this ticket to the station attendant, or give it to the conductor/put it into the box at the station if you're disembarking at an unmanned station.
   2. Numbered ticket (整理券 aka Seiri-ken): When you board, there may be a small dispenser that dispenses a numbered ticket. Grab one, this will correspond to the monitor at first car that will show the price. When you reach your stop, put the ticket along with the money (in coins) into the box at the front of the car. Sometimes, you may be directed to pay at the station window instead, if stopping at a major manned station. If you need change, there will often be a change machine next to where you make the payment.
   3. Limited express trains: If the unmanned station has a ticket machine for limited express, use it, simple as that. Otherwise, board the train, and the conductor or staff will approach you for payment. When you disembark, you may have to hand it to the conductor, or to the station attendant.
2. Manned station: There are two different types of manned stations
   1. Fully-manned station: These are the most convenient, as they will have a manned green ticket window office/green ticket vending machine (or the equivalent for your applicable regional JR company) to buy local or reserved seating limited express JR tickets.
   2. 簡易委託駅 (aka kantaku station): A station that is manned by another operator than the railroad company using the station. These lack a green window, and also may not have ticket machines. Instead, the station window can sell you local, and also only unreserved seating (自由席 jiyuu-seki) limited express tickets.
   3. Beware of operating hours: Pretty much every station in Japan has operating hours, from the ticket counter to even the ticket machines. However, in the countryside this can be even more restricted. When you arrive at a station, take note of the operating hours for the ticket window and machines. Sometimes, the operating hours can be strange (i.e. closed on weekends). If your station window is closed for the day, it will be treated the same as an unmanned station.
3. Special tickets
   1. Boarding voucher: Kind of rare, but this is just a small stamped piece of paper declaring your station of departure. You typically receive these from the station window. Hand it to the conductor on the train, tell them your destination, and pay.
   2. One day pass (or two-day pass, if offered): Typically only offered at the station window, but some local railway companies do sell them on the train. Show them to the conductor/station window when entering/exiting.

Boarding

• Many local trains in the countryside are what are called one-man cars, meaning that there is only one conductor on board. As a result, the way you board and disembark is very specific.
  • When boarding or disembarking, you do so at the first car (first car is the car that is headfirst in the direction of travel). You may need to press the button to open the door, as the train may not open its doors automatically.
  • Boarding: Enter via the rear-most door of this first car
  • Disembark: Exit via the forward-most door of this first car.

Bus

Paying for your ticket

1. Paper ticket: Sometimes, you can purchase bus tickets in advance for certain routes (i.e. routes to-from a station/airport, or some tourist destination) and pick them up from either terminus.
2. Numbered ticket (整理券 aka Seiriken): Same as a train, this is the most common method of payment.
3. Expressway bus: Many, especially long distance ones, are reservation-only. You can reserve online or by phone, and pick them up at JR ticket offices (if its a JR bus), major bus terminals, or konbini
4. Fixed fee: A route with a fixed fee regardless of boarding or disembarking location. These are uncommon but you may encounter them. Simply board, and pay with change or IC (if supported) when you get off.
5. Day pass: Some bus companies offer a day pass. You can buy these from the bus driver when you board.