You'll get the best view of Mount Fuji just after passing Shizuoka Station. Once your train has passed through Shizuoka Station, you'll go through a tunnel and pass by the Fuji River.

Yes, you can see Mt. Fuji when traveling from Tokyo to Kyoto, but only if you sit on the correct side of the Shinkansen (bullet train). You should request a seat on the "E" side (mountain side) in standard cars or the "D" and "E" seats in Green Cars. The mountain typically appears about 40 to 45 minutes after departing Tokyo, specifically between the Shin-Fuji and Shizuoka stations. However, visibility is highly dependent on the weather; the mountain is often shrouded in clouds, particularly during the humid summer months. The best chances for a clear view are during the early morning hours in autumn or winter when the air is crisp and the sky is clear. Even with a good seat, the view is fleeting, lasting only a few minutes as the train speeds past at over 200 km/h. If you are traveling in the opposite direction (Kyoto to Tokyo), you should sit on the left side of the train (A-side seats) to catch a glimpse of Japan's most iconic peak as you approach the Shizuoka region.