The Japan Rail (JR) Pass offers incredible value, but it does not cover every train on the network. The most notable exclusions are the Nozomi and Mizuho Shinkansen services, which are the fastest categories on the Tokaido, Sanyo, and Kyushu lines. While you can technically ride these by paying a special supplemental surcharge (introduced in late 2023), they are not included in the "free" base pass. Additionally, the pass is generally only valid on JR-branded lines; it does not cover private railways (such as Odakyu to Hakone, Tobu to Nikko, or Kintetsu between Osaka and Nagoya), nor does it cover the Tokyo Metro or Osaka Metro systems. Some JR trains that run over private tracks, like the "Fuji Excursion," require a supplemental fare for the non-JR portion of the journey. Most "Liner" trains and some "Limited Express" trains with specialized "Green" (First Class) or "Gran Class" seating require extra payments if you only hold an Ordinary JR Pass. Finally, the pass does not cover highway buses or the majority of local city buses not operated directly by the JR Group.