Japan’s railways are not all operated by the same company. JR lines, private railways, and subways are run by different organizations, and each has its own fare and ticket system.
JR developed from the former Japanese National Railways, which was operated by the government. JR is now made up of private companies divided by region, but many Japanese people still have the impression that JR is somehow closer to the government, while private railways are seen as private-sector companies.
JR operates many routes connecting different cities and rural areas. Japan’s Shinkansen bullet trains are also operated by JR companies.
In Japan, the term “private railway” usually refers to a privately operated railway other than JR. In large cities such as Tokyo and Osaka, major private railway companies operate many lines connecting city centers with the suburbs.
There are also smaller private railways in rural areas. These may have fewer trains, more unmanned stations, and routes where common IC cards cannot be used.
Subways mainly run underground in large cities. They may be operated by a local government or a private company, but from a passenger’s point of view, using them is not very different from using JR or a private railway.
The most noticeable difference appears when you change from one railway company to another. Since the companies have separate fare systems, the fare may be calculated separately.
Even when two stations have the same or similar names, you may need to leave one ticket gate and enter through another gate to transfer from JR to a private railway or subway.
However, many routes now accept transit IC cards such as Suica. The fare is calculated automatically when you touch the card at the ticket gate, so Japanese passengers usually do not think very much about which company operates each line.
Still, Suica and other widely used IC cards do not work on every railway in Japan. Some smaller regional lines accept only their own local cards, while others do not accept IC cards at all.
The main differences between JR, private railways, and subways are who operates them and whether their fares and tickets are part of the same system. When travelling in Japan, checking the route and line names on a journey-planning app is usually enough to get where you need to go.