Shinkansen (bullet train) from Tokyo Station or Shinagawa Station to Kyoto Station
Nozomi Shinkansen for the fastest direct trip
Hikari Shinkansen for a slightly slower direct option
Kodama Shinkansen for the slowest option with more stops
Domestic flight from Tokyo Haneda Airport or Narita Airport to Osaka Itami Airport or Kansai International Airport, then train or bus to Kyoto
Highway bus from Tokyo to Kyoto
Rental car or private car transfer via the Tomei or Meishin expressways
Overnight bus from Tokyo to Kyoto
Local train combinations using JR lines and transfer stations