The JR Nara line takes 45 minutes by express train or 70 minutes if you catch a local train from Kyoto Station. It's covered by the JR Pass but the price is 690 yen if you don't have one. This is the best way to get from Kyoto to Nara if you have the Japan Rail Pass.
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The JR Pass is valid on all Shinkansen services in all the Shinkansen lines, except for the Nozomi and Mizuho services on the Tokaido and Sanyo Shinkansen lines. You will not have access to the trains with the fewest stops on the Tokaido and Sanyo lines.
The Japan Rail Pass is valid for West JR Bus company, which operates the Takao Keihoku Line. This line runs between Kyoto station and Shuzan. You will be able to go to Ninnaji Temple and Ryoanji Temple.
The 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.
Exclusively for foreign tourists to Japan, the JR West Kansai Pass provides unlimited travel on local JR trains and West JR buses in the Kansai region around Osaka, Kyoto, Nara, Kobe, and more for one to four days.
You may bring up to 2 baggage items with a total length, width, and height of up to 250 cm (up to 2 meters in length) and a weight of up to 30 kg. However, please reserve a seat with an oversized baggage area or oversized baggage compartment when carrying on oversized baggage.
With the Japan Rail Pass, you can ride on all JR trains, including the Shinjuku Line, without paying additional fares. However, it's important to note that the Japan Rail Pass is not valid on other non-JR train lines, such as private railways or subways.
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.
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 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.
You can use Icoca/Pasmo/Suica for all trains, subways and buses in Osaka. You can also use Icoca/Pasmo/Suica at many shops, especially convenience stores. You can use Icoca/Pasmo/Suica in other parts of Japan as well. Buy Icoca cards from vending machines at JR stations in Osaka.
If you are traveling to multiple cities in Japan and plan on using the bullet train (Shinkansen) or other long-distance trains (local, express or limited-express trains), then the JR Pass can be a cost-effective option.
The Suica can be used on JR East lines in the Tokyo metropolitan area as well as for subways, buses and the Tokyo Monorail that connects Haneda Airport with Tokyo.
Tokyo to Fuji Five LakesTake the JR Chuo Line from Shinjuku Station (Tokyo) to Otsuki Station (Azusa trains, covered by the JR Pass). Once at Otsuki, take Fujikyu Railway to Kawaguchiko Station (not covered by the JR Pass).
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.