Take a Hikari train along the JR Tokaido Shinkansen from Kyoto to Shizuoka (every second Hikari stops at Shizuoka) and transfer to the JR Wide View Fujikawa limited express train to Fujinomiya. The entire one way journey takes about 2.5 hours, costs around 11,500 yen and is fully covered by the Japan Rail Pass. If there is no connecting limited express train, you can also take local trains via Fuji Station, which adds just a little bit to the travel time and reduces the fare by a few hundred yen.
By train and bus
3.5 h
¥11,000
Take a Kodama train along the JR Tokaido Shinkansen from Kyoto to Shin-Fuji Station (140 minutes, about 10,500 yen). From Shin-Fuji Station, there are 3-4 buses per day bound for the Fuji Five Lakes, which stop at Fujinomiya Station (35 minutes, 570 yen) and the Shiraito Falls (1 hour, 1080 yen) along the way. The shinkansen is fully covered by the Japan Rail Pass, but the bus is not.
By overnight bus
8 h
¥7,900
Fujikyu Bus and Kintetsu Bus operate overnight buses between Osaka and the Fuji Five Lakes, which stop at Kyoto and Fujinomiya Stations along the way. The one way trip between Kyoto and Fujinomiya takes about eight hours and costs 7900 yen.
Above fees and schedules are subject to change. Be sure to check current yen exchange rates.
Another transportation hub is Shin-Fuji Station along the Tokaido Shinkansen, which is served only by Kodama trains. From Shin-Fuji Station, there are infrequent buses to Fujinomiya Station, Shiraito Falls and the Fuji Five Lakes. Note that local trains stop at Fuji Station, which is 1.5 kilometers away and not served by many of the buses in direction of the Fuji Five Lakes.
The Mount Fuji West Side Story Passport provides two days of unlimited use of buses on the west and north side of Mount Fuji for 3500 yen, including the bus between Shin-Fuji Station and Kawaguchiko Station and the tourist buses around Lake Kawaguchiko and Lake Saiko. In addition it provides discounts at selected tourist attractions, shops and restaurants. The pass can be purchased at Shin-Fuji, Fujinomiya, Kawaguchiko and Fujisan stations.
Despite all the buses that run though the area, the connections around Fujinomiya may not be very convenient for those wishing to visit multiple sites in a day. Those visitors may be better off exploring the area by rental car. Rental car outlets can be found around Shin-Fuji and Kawaguchiko Stations.