By train
Gero Onsen's train station, Gero, is located on the JR Takayama Line.
The easiest method of reaching Gero Onsen is to take a shinkansen bullet train to Nagoya and transfer there to the Wide View Hida limited express train. From Tokyo the run takes about 3 1/2 hours via Nozomi at a cost of ¥13500. The Japan Rail Pass is NOT valid for Nozomi trains; using the Hikari service will take about four hours, including transfer time.
Gero is a 2 1/2 hour ride from Kyoto using the Nozomi to Nagoya ¥8880.
If you take local trains from Nagoya, the ride will take approximately three hours, with transfers required at Gifu and Mino-Ota, at a cost of ¥2210.
If you decide to take all local trains from Tokyo i.e. while using a Seishun 18 Ticket, you will need to depart Tokyo very early in the morning, or stay over at an intermediate stop, since the ride to Gero will take about nine hours. A 7:00 departure from Tokyo will have you arriving in Gero after 16:00. Without the Seishun 18 ticket this will cost ¥7670.
Whatever method you choose, the views of the valley and the Hida River below as you approach Gero station are spectacular.