While the metro lines do no accept the JR Pass, other IC Cards, such as the Pasmo and Suica, may be used. These cards give you access to almost any train or bus in Tokyo, and are a perfect complement to the JR Pass.

A common point of confusion for travelers in Japan is whether the Japan Rail (JR) Pass covers city subways or metro systems. The short answer is no; the JR Pass is generally not valid on subway or metro lines in cities like Tokyo, Kyoto, or Osaka. These systems are operated by private companies or municipal governments (such as Tokyo Metro or Toei Subway) that are entirely separate from the Japan Railways Group. However, the JR Pass is valid on JR-operated urban lines, such as the famous Yamanote Line (the loop line) and the Chuo-Sobu Line in Tokyo, or the Osaka Loop Line. These lines often cover many of the same major tourist districts as the subways. To use the actual subway, you must purchase a separate ticket or use an IC card like Suica or Pasmo. While the JR Pass is an incredible value for long-distance Shinkansen travel between cities, it is not an all-access pass for local city transit, and you should expect to spend a few extra dollars a day on local subway fares to reach specific neighborhoods not served by JR stations.