Can I use the JR Pass in Kyoto? Yes, to a limited extent. JR lines run to the west and south of Kyoto, with access to highlights such as Arashiyama, Fushimi Inari and Uji. Additionally, a local JR bus runs from Kyoto station to north Kyoto.
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The Nara Line to Nara, Uji, and Inari Station (close to the Fushimi Inari Shrine) The Sanin Main Line, also called the Sagano Line, which connects to Saga-Arashiyama, the Arashiyama Bamboo Grove and the Sagano Scenic Railway (not included with the JR Pass).
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.
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.
With your pass, you can take unlimited rides on most shinkansen (bullet trains), as well as on rapid, express and local JR trains. Outside urban centers such as Tokyo and Osaka, the pass is best used to cover distance, as it does not include municipal subways and private suburban lines.
If you calculate that your travel costs will be lower if you buy individual tickets for each journey, then it's not worth buying a JR Pass. However, if you take into account journeys on Shinkansen high-speed trains or other means of transport, the savings you make become substantial.
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.)
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.
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.
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.
With a medium stay of 4-5 days in Kyoto, you'll have the opportunity to delve deeper into the city's rich history and culture. This extended duration allows you to venture beyond the most famous attractions and explore some of Kyoto's lesser-known gems.
A standard fee for a one-way Tokyo to Kyoto ticket is around 160 USD during peak seasons and 100-120 USD off peak, although the price heavily depends on such factor as what travel class you prefer or do you purchase a ticket with reserved or unreserved seats.
The shinkansen (bullet train) is the best way to travel between Tokyo and Kyoto. It takes around 2 hours and 15 minutes and costs Y13,080 between Tokyo and Kyoto(non-reserved seat). You don't need to reserve seats on the shinkansen if you travel outside of peak travel hours and outside of peak travel seasons.
The Japan Rail Pass can be purchased outside of Japan in advance. It is necessary to purchase an Exchange Order before your departure. After entering Japan, you will have to obtain your JR Pass by submiting your Exchange Order at a JR office or designated Rail Station.
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.