Aside from cash, the following methods of payment are available: One-Day Ticket (such as the Subway & Bus 1-Day Pass)IC Card (such as PiTaPa, ICOCA, Suica, & PASMO)
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Smart cards like Icoca, Suica and Pasmo are valid across Japan, so don't worry about which one you buy. You can use Icoca/Pasmo/Suica for all trains, subways and buses in Kyoto. You can also use Icoca/Pasmo/Suica at many shops, especially convenience stores. Buy Icoca cards from vending machines at JR Kyoto Station.
But not on Eizan Railway Line or on Kyoto City Bus. You should be able to recharge your card with the machines accepting IC cards including ICOCA and SUICA/PASMO. The Suica is valid on everything in Kyoto except the City Bus and Eizan Railway. You can recharge it using the machines as you do in Tokyo.
A Pasmo card is the same as a Suica. You can use it for trains, subways and metro stations and some buses. It is also a tap on card. You can purchase a Pasmo at most stations ( including subway stations) at a vending machine by tapping ENGLISH on the machine and following the instructions provided.
Every station has multilingual ticket machines where you can buy a one-way fare ticket, or you can use a rechargeable IC card to swipe in and out of the ticket gates. Tokyo Metro and Toei have teamed up to offer a subway pass for tourists that can save you some yen, as well as being super convenient.
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.
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.
The stations are usually crowded and once you've found the right ticket machine (and there are many) and waited in line to buy the fare ticket you need you'll have probably missed your train. The Suica card is by far the easiest way to use public transportation.
Can we just swipe the same card 3 times while going thru the gate? You need 3 cards. Every individual needs their own cards to use train. Scanning the card three times to allow three people, or giving the card back so three people could use it would not work because of the design of the system.