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.
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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.)
PASMO is a convenient prepaid transportation card that contains an integrated-circuit (IC) chip, allowing the user to enter the subway by simply placing the card over a PASMO card reader located on the fare gates. The card is rechargeable and can be used over and over.
Ueno-Tokyo Line services running from JR Ueno Station are all southbound. At JR Ueno Station these services depart from platforms 7, 8, and 9. As this is a JR line it is covered by the Japan Rail Pass.
Ownership and operation: JR trains are owned and operated by the Japan Railways Group, which is a conglomerate of regional railway companies across the country. Metro trains, on the other hand, are owned and operated by various municipal governments in major cities like Tokyo, Osaka, and Nagoya.
Tokyo Metro and Toei Subway operate the subways in Tokyo. At the entrance to each station, you will see the subway sign and the name of the subway station. Be sure to remember the station name, number and line color (circular colored outline) of the subway line you want to ride.
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.
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 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.
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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.
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).
With your Japan Rail PassThe Hikari and Kodama trains on the Tokaido Shinkansen lines are covered by the Japan Rail Pass, and they can take you from Tokyo to Osaka in about 3 to 4 hours. In Tokyo, you can catch the Shinkansen either at Tokyo Station or Shinagawa Station, and then arrive to Shin-Osaka Station in Osaka.
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.)