You can use the Japan Rail (JR) Pass for the Fuji Excursion limited express train, but it only covers a portion of the journey. The train runs on two different rail networks: the JR East line (from Shinjuku to Otsuki) and the private Fujikyu Railway line (from Otsuki to Kawaguchiko). While your JR Pass fully covers the segment from Shinjuku to Otsuki, it does not cover the Fujikyu portion. In 2026, JR Pass holders must pay a supplemental fare (approximately ¥1,140 to ¥1,600 depending on the station) for the section between Otsuki and Lake Kawaguchiko. This supplement is usually collected by the conductor on the train or can be paid at the station. However, if you have the JR TOKYO Wide Pass, the entire Fuji Excursion journey is fully covered with no extra fees, making it a better value for those specifically planning a 3-day trip to the Fuji Five Lakes area from Tokyo.