With your Japan Rail PassThe Hikari and Kodama trains on this line are covered by the pass, and can take you from Shin-Osaka Station in Osaka to either Shinagawa Station or Tokyo Station in Tokyo in under 3 hours.
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Furthermore, the JR Pass can be used on the Tokyo Monorail, the Yamanote line (Tokyo Metro), the Aoimori Railway between Aomori and Hachinohe*, the Ainokaze Toyama Railway between Toyama and Takaoka*, Narita Express from Narita Airport to Tokyo and the IR Ishikawa Railway line between Kanazawa and Tsubata*.
With your Japan Rail PassThe cities of Tokyo and Kyoto are linked to each other by the JR Tokaido Shinkansen Line. A one-way trip from Tokyo Station to Kyoto Station on a Hikari or Kodama train costs 13,080 yen (unreserved seat) or 13,800 yen (reserved seat), but is completely free with a JR Pass.
As these trains are not covered by JR pass, a one-way Osaka to Tokyo train ticket costs around 160 USD in peak season and around 120 USD off peak. Read more about the Japanese train tickets here.
Validity. The pass is valid on almost all trains operated on the nationwide network of JR (Japan Railways), including shinkansen, limited express, rapid and local trains. The map below shows the major train lines that are covered by the pass.
The JR Kansai Area Pass is a rail pass for exclusive use by foreign visitors to Japan, providing unlimited travel on local JR trains and buses in the Kansai Region around Osaka, Kyoto, Nara and Kobe, as well as on the Haruka limited express train to/from Kansai Airport.
JR East operates the most convenient train lines for moving around central Tokyo, and you can use your JR Pass on all of these metro services. The rest of the 13 Tokyo subway lines that run in and around the Yamanote line are operated by companies other than JR East.
The JR Pass does not allow you to ride on subways or trams within cities. However, most big cities have a few JR lines that you can use to go around, like the Osaka Loop or Kanjo line and the Tokyo Yamanote line, for example.
The Japan Rail Pass is valid only on a portion of the travel from Tokyo to Mount Fuji. At Shinjuku Station, take the JR Chuo Line to Otsuki Station. This leg takes around 1 hour, and is covered by your JR Pass. At Otsuki Station, you must transfer to the Fujikyu Railway Line to reach Kawaguchiko Station.
Unless you plan to ride a LOT of JR trains during your trip, you'll almost certainly save money by buying individual train tickets instead a Japan Rail Pass. You can buy shinkansen tickets online (before or after arrival) on the Tokaido, Sanyo and Kyushu lines (between Tokyo,Nagoya, Kyoto, Osaka, Hiroshima and Hakata).
The PASS is valid on all Japan Railways (JR) Group Shinkansen “bullet trains” (except for the “NOZOMI” and “MIZUHO” trains), limited express trains, express trains, and local trains (Green Car passes are valid for Green Car travel) in addition to the BRT (Bus Rapid Transit system).
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.)
You may get some value from some day type passes, but not from a nationwide rail pass. (if you were going as far a Kyoto, it would be about breakeven for you). A JR pass is of no value if you're only going to be in Tokyo. If you plan to arrive at NRT - http://www.jreast.co.jp/e/suica-nex/ - is a good value.
For a limited time only, you can buy a Japan Rail Pass from certain train stations and airports in Japan. Travelers should be aware it is more expensive to buy a JR Pass in Japan than to purchase the pass online.
Your JR Pass can cover your entire journey from Narita Airport to Osaka. From Narita Airport, take the JR Narita Express to Tokyo Station. Trains depart approximately every two minutes.
The Japan Rail Pass gives you access to JR train lines countrywide, with very few exceptions. With your pass, you can take unlimited rides on most shinkansen (bullet trains), as well as on rapid, express and local JR trains.
The Shinkansen service which runs from Shin-Osaka Station to Kyoto Station is the fastest way and it's covered by the JR Pass. The bullet train time is only 15 minutes. If you don't have a JR Pass, the Shinkansen price for this journey is 1,420 yen.
Yamatoji rapid trains run every hour between Osaka and Nara from JR Osaka Station. The one-way trip takes 45 minutes and is covered by the JR Pass (it costs 800 yen without one).
The JR pass is only worth it if you travel through different cities, if you are just travelling to Tokyo to Kyoto for example, I would just pay on the Suica. You can do the online calculator or just use google to calculate which trip is easier - paying individually on Suica or getting a JR Pass.
Shinkansen or bullet trainThe fastest way to travel from Osaka to Tokyo is via the Tokaido Shinkansen's Nozomi train. In only about 2 hours and 30 minutes, it can take you from Shin-Osaka Station in Osaka to Tokyo Station or Shinagawa Station in Tokyo.