All JR Group Railways-Shinkansen”bullet trains” (except any reserved or non-reserved seat on “NOZOMI” and “MIZUHO” trains) limited express trains, express trains, and rapid or local trains, and the BRT. (With some exceptions)
*JAPAN RAIL PASS holders can also use the Tokyo Monorail.
*Aoimori Railway services between Aomori and Hachinohe (but only for travel on local or rapid service trains encompassing the segments between Hachinohe and Aomori, Aomori and Noheji, and Hachinohe and Noheji. Travel is not covered if you disembark at any other station on the Aoimori Railway line other than Aomori, Noheji, and Hachinohe.)
*The IR Ishikawa Railway Line between Kanazawa and Tsubata. (However, travel must be conducted on local or limited express trains and must encompass the full segment between these two stations. Travel is not covered if you disembark at any station on the IR Ishikawa Railway line other than Kanazawa or Tsubata.)
*The Ainokaze Toyama Railway Line between Toyama and Takaoka. (However, travel must be conducted on local trains and must encompass the full segment between these two stations. Travel is not covered if you disembark at any station on the Ainokaze Toyama Railway line other than Toyama or Takaoka.)

Nationwide JR Route Map Shinkansen Bullet Train Railway Map

Local lines of JR Bus (excluding some local lines) (Pass validity for particular routes is subject to change.)
(JR Bus : JR Hokkaido Bus, JR Bus Tohoku, JR Bus Kanto, JR Tokai Bus, West Japan JR Bus, Chugoku JR Bus, JR Shikoku Bus, JR Kyushu Bus)
*The PASS is not valid for travel on express bus routes operated by JR Bus.

Only the JR-WEST Miyajima ferry is covered.
*Hydrofoil ferry service operated by JR-KYUSHU between Hakata and Pusan (Korea) is not covered.

The JAPAN RAIL PASS is not valid for any seats, reserved or non-reserved, on “NOZOMI” and “MIZUHO” trains on the Tokaido, Sanyo and Kyushu Shinkansen lines. (The pass holders must take “HIKARI,” “SAKURA,” “KODAMA,” or “TSUBAME” trains.) If you use a “NOZOMI” or “MIZUHO” train, you must pay the basic fare and the limited express charge, and for a Green Car, the additional Green Car surcharge.

In addition, if you use the GranClass car of the Tohoku Shinkansen, Hokkaido Shinkansen and Hokuriku Shinkansen, you must pay the limited express charge and the GranClass car surcharge.

Note also that passengers using JR trains on non-JR lines must pay additional fares and charges for sections traveled on such lines. Some JR trains use the lines of private railways for direct services.