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 the difference between the Japan Rail (JR) network and the various city Metro/Subway systems. The Japan Rail Pass does not include access to the Tokyo Metro, the Toei Subway, the Osaka Metro, or the Kyoto Subway. These are separate private or municipal entities with their own ticketing systems. The JR Pass is valid only on lines operated by the JR Group, which include the Shinkansen (bullet trains), limited express trains, and local JR lines (like the famous Yamanote Line loop in Tokyo or the Osaka Loop Line). While you can get to most major districts using only JR lines, you will often find that a Metro line provides a more direct route to specific landmarks or hotels. To bridge this gap, most travelers use a rechargeable IC Card (like Suica or Pasmo) to pay for Metro fares as they go. However, there are some regional exceptions; for example, the JR Pass can be used on the JR-operated Miyajima Ferry in Hiroshima and the JR bus lines in certain cities, but for underground city subways, you will always need a separate ticket or IC card.