Train from Mount Fuji to Kyoto

Since Kawaguchiko station is not a JR station, you can't use JR trains all the way. But you can use it most of the way.

From Kawaguchiko station, take the Fuji Kyuko line to Otsuki station. From there, you can take the JR Limited Express "Kaiji" to Shinjuku station. From Shinjuku station, take the JR Chuo line express to Tokyo station. Finally, take the Shinkansen from Tokyo to Kyoto station.