Guide and information of Japan travel, with access and transportation from Tokyo to Takayama by Shinkansen train, highway bus.
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TOKYO - TAKAYAMA
This site would like to explain several routes (No1, No2, No3 and No4) between beautiful mountain town Takayama and one of the biggest city in the world, Tokyo.
No.1. FOR JAPAN RAIL PASS HOLDERS
Limited Express (Wide View Hida) and Shinkansen (bullet train, super express)
For JR PASS holders, this is by all means the easiest and the fastest way to travel between two places (Takayama and Tokyo).
The Limited Express called Wide View Hida has, as you assumed, has such a great view along Hida River between Mino-Oota and almost all the way to Takayama (precisely, the river goes through Takayama is called Miyagawa which joins to Jintsuu River and finally to the bay of Toyama). Especially those who can reserve the most front seat, wish you enjoy the train driver's view. There are 10 train service everyday.
Shinkansen from Nagoya to Tokyo has every 10 minutes freaquent train (all 16 cars with capacity 1,323 seats). Nozomi is the fastest takes 1hour and 45 minutes, Hikari is a bit slow takes 2 hours, and Kodama is the slowest Shinkansen takes 2 hour and 50 minutes between Nagoya and Tokyo.

Wide View Hida : 2 hours and 20 minutes. JPY5,870. 10 train service a day.

Nozomi (Hope) : What goes/runs/travels faster than Hikari (light). We shall better to have Nozomi to live. 1 hours and 45 minutes. JPY10,780. Every 10 minutes or less, which means that there are 6 or more trains every 1 hour.

Hikari (Light) : The fastest object runs in the universe. 2 hours. JPY10,580. There are 2 trains every 1 hour. JR Tokai (JR Central) sells advance tickets called Hayatoku-Kippu as low as JPY9,200 (one week piror purchase necessary).

Kodama (Sound) : Speed of sound is used to be representative of fastness. 2 hours and 50 minutes. JPY7,900 (Puratto Kodama normal seat) or JPY8,900 (Puratto Kodama green car, 1st class seat).
No.2. HIGHWAY BUS
Highway Bus direct from Takayama to Shinjuku
There are 5 buses a day. JPY6,500 one way, takes 5 hours and 30 minutes.
Bus from Takayama to Matsumoto
For those who would like to enjoy stopping over at Matsumoto (and Kita-Alps, North-Alps), you may take one of 4 buses a day from Takayama to Matsumoto (JPY3,100 one way). Matsumoto is directly connected by JR trains to Shinjuku (and some all the way to Tokyo).
No.3. SEISHUN 18 KIPPU
Seishun 18 Kippu
Only available during students holiday time (Winter, Spring and Summer). It can be JPY2,300 one way between Takayama and Tokyo with best minimum 5 changes as shown below (please note that usually needed 6 - 7 times transfers). Hyperdia would support finding your best time tables.

Takayama 05:26 - 08:26 Gifu 08:31 - 09:45 Toyohashi 09:49 - 10:24 Hamamatsu 10:29 - 11:43 Shizuoka 11:53 - 13:05 Atami 13:16 - 15:06 Tokyo
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