From Tokyo to Kyoto, high-speed train is the way to go. The famous Tokaido Shinkansen links Tokyo to Kyoto, with the fastest travel time of about 2 hours. Bullet trains run frequently on this Shinkansen route. The fastest train Nozomi cannot be taken by JR Pass. But you can use the JR Pass to take Hikari trains and Kodama trains from Tokyo to Kyoto.
Nozomi train: this is the fastest train running from Tokyo to Kyoto, with the travel time of about 2 hours. Japan Rail Pass cannot be used to take Nozomi trains.
Hikari train: this is the second fastest rail service with the Tokyo to Kyoto duration of about 2.5 hours.
Kodama train: this is the slowest high-speed service on from Tokyo to Kyoto, with the travel time of about 4 hours.
A round-trip fare from Tokyo to Kyoto by shinkansen takes about 27000 yen, almost the same fare of a 7-day JR Pass. If you plan to travel to other places of the country or use the metro in the city, buying a JR pass would be much cheaper and more convenient.
You can take shinkansen at Shinagawa Station, which is near Haneda Airport, Shinjuku Station and Ikebukuro Station.
Shinkansen services to Tokyo depart from Kyoto Station. Kyoto Station is the transport hub of the city, serving JR Railways (including The Tokaido Line). Outside the stations of the NRT and MTR Umaru Line are the city bus terminus and the interchange of long distance and overnight high-speed buses.
Tokyo Station is one of the largest and busiest train stations in Japan. Over 3,000 trains stop at this station per day.
Trains in Japan offer three classes of seat: ordinary seat, green car seat and gran class seat.