From Tokyo
to Shinano-Omachi
Take the JR Nagano Shinkansen from Tokyo to Nagano (100 minutes, around 8000 yen one way) and then a bus directly to Ogizawa along the Alpine Route (105 minutes, 2500 yen one way). The Japan Rail Pass covers the shinkansen, but not the bus.
Alternatively, take the Azusa Limited Express from Tokyo's Shinjuku Station to Matsumoto (2.5 hours) and transfer to the JR Oito Line to Shinano-Omachi Station (1 hour). The one way journey costs around 7500 yen and is fully covered by the Japan Rail Pass. A small number of Azusa limited express trains run all the way to Shinano-Omachi.
to Toyama
Take the JR Joetsu Shinkansen from Tokyo to Echigo-Yuzawa (75 minutes), followed by a ride on the Hakutaka Limited Express to Toyama (2 hours). The one way fare is about 11,500 yen. Note, however, that the Hakutaka uses non-JR tracks between Echigo-Yuzawa and Naoetsu. Therefore, Japan Rail Pass holders will have to pay a supplement of 1450 yen. A fully covered, alternative route leads via Nagaoka, using the JR Joetsu Shinkansen (100 minutes) and JR Hokuetsu Limited Express (2 hours).
From Osaka/Kyoto
to Toyama
The one way journey by direct JR Thunderbird Limited Express trains takes about 3 to 3.5 hours, costs around 8000 yen and is fully covered by the Japan Rail Pass.
to Shinano-Omachi
Take the JR Tokaido Shinkansen to Nagoya (1 hour), the JR Shinano Limited Express to Matsumoto (2 hours) and the JR Oito Line to Shinano-Omachi (1 hour). The one way fare is about 11,000 yen and fully covered by the Japan Rail Pass.
From Nagoya
to Toyama
The one way journey by direct JR Shirasagi Limited Express trains takes about 4 hours, costs around 8000 yen and is fully covered by the Japan Rail Pass.
to Shinano-Omachi
Take the JR Shinano Limited Express to Matsumoto (2 hours) and the JR Oito Line to Shinano-Omachi (1 hour). The one way fare is about 6,500 Yen and fully covered by the Japan Rail Pass.
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