Is there any train that needs additional payment with a Japan Rail Pass ?

With a Japan Rail Pass, most of your journeys are free. There are only a few exceptions. Indeed, travel on JR Group trains that connects directly with non JR railway will require additional payment of basic fares and charges for the section operated by the other company. In that case, you will have to pay on the train or at the station. Please find below the itineraries and the train name.

If you ride the FUJI EXCURSION 1 and 3 from Shinjuku station to Kawaguchiko or the FUJI EXCURSION 16 and 20 from Kawaguchiko Station to Shinjuku station you will need to pay an additional charge of 1140  yens. Click here to find more information about this train. 

If you ride the SPACIA Nikko to Tobu Nikko Station or the SPACIA Kinugawa to Kinugawa Station from Shinjuku you will need to pay an additional charge of 2000 yens

Please note that to reach Amanohashidate, you will have to ride on the Kyoto Tango Railway. The additional fare from Kyoto to Amanohashidate/Toyooka is 2870 yens, from Shin Osaka to Amanohashidate 1520 yens.

To go to Tottori from Kyoto or Okayama, the trains Super Hakuto and Super Inaba are using a private section between Kamigori and Chizu. Additional fare is required ( 1820 yens).

You will find the same thing (additional charge) with the Super View Odoriko and the Odoriko, a direct Express from Tokyo to Izukyu Shimoda, from Nagoya to Shingu with the Wide Express Nanki, or from Nagoya to Toba with the Limited Express Rapid Mie, from Shinjuku to Gotemba, with the Asagiri train and in some other very few lines.

These informations can be useful when you are doing your travel plan with Hyperdia. Please pay attention on the train name.