If you want to save the time and save your money to stay hotel, overnight transfer is considerable. Many travelers move among Tokyo, Kyoto and Osaka. We have a few ways to take overnight transfer among these cities by Japan Rail Pass too. I would like to tell about it in this post.
Overnight train is actually not realistic option in these days. Many overnight trains were discontinued. There is no scheduled overnight train service just between Tokyo and Osaka/Kyoto. But there are some options
Sunrise Seto and Sunrise Izumo
These trains connect Tokyo, Takamatsu and Izumoshi. The train bound for Tokyo can be used overnight option.
These trains stop at Osaka at 00:34 and arrive at Tokyo at 07:08. Especially Nobi Nobi seat on these trains is fully covered by JR Pass. These trains do not stop at Kyoto. You have to go back to Osaka. It is 30 minutes away from Kyoto by Special Rapid Service train.
Sunrise Seto and Sunrise Izumo from Tokyo go by Osaka and Kyoto because it it too early. You can get off this train at the first station which is Himeji at 05:24. You can take Special Rapid to go back to Osaka and Kyoto.
However you have to take a risk if you use this train in your trip plan. Because you cannot reserve a seat or berth online. That means you have to book upon arrival. All spaces may be booked out at the time of booking. It is hard to say about the availability but I am not surprised if all spaces are booked out a few days prior to travel date. You must prepare back up plan for the case of booked out if you take this option in your trip plan.
Rapid Moonlight Nagara
If you travel in the peak period, you may be able to take overnight rapid train, Moonlight Nagara:
This train is operated between Tokyo and Ogaki. Ogaki is located between Naogya and Kyoto. You have to transfer to other trains at Ogaki or Nagoya to get Kyoto or Osaka. Moonlight Nagara is a sort of local train. But all seats are reserved seat. You cannot take this train without reservation. And it is very hard to book because of popularity. If you use Japan Rail Pass, you can get on this train with no extra charge. However it is very challenging to book a seat on this train after you arrive in Japan.
This train is operated in peak season only. You can find the operation dates in Category of Seasonal trains schedule.
There are many overnight bus services running between Tokyo, Osaka and Kyoto. JR pass used to cover some overnight bus but it does not cover any overnight bus at all now.
Willer Travel operates lots of overnight bus. Please see the link below to find more information.
Actually I am not a big fan of bus. I have never taken Willer Bus before. I cannot answer any inquiries about this bus service.