Hello! I will be getting the JR Pass and am planning to take a bullet train from Sapporo to Tokyo. I tried using Hyperdia.com and it seems the earliest available train is 4pm and I will only reach Tokyo the next day at 9am. Is this information correct?
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No, there is no overnight train now.
See for example:
http://bit.ly/2djKrD5
But it would take you about 8½ hours by train - completely murdering the whole day. Why not fly? You can take a low cost carrier like Jet Star, Peach or Vanilla Air, and fly one way for as low as $50 - and arrive in less than 2 hours.
Taking the train only makes sense if you are stopping off somewhere along the way.