Japan Railways have operated many overnight trains before. But in these days, many of those overnight train services were discontinued. Now the choice is very limited.
The list of overnight trains
Japan Rail Pass does not cover any accommodation fee for overnight trains. Most of overnight trains have berth and bedroom. So if you want to take this train, you have to pay extra for this accommodation on top of JR Pass. But these following trains have an accommodation that you can take by Japan Rail Pass without any extra charge. Please find more details on each page of trains.
Limited Express Sunrise Seto and Sunrise Izumo
“Seto” runs between Tokyo and Takamatsu and “Izumo” runs between Tokyo and Izumoshi. These trains run as coupled between Tokyo and Okayama. Those trains offer Nobi Nobi seat which is very simple berth. This Nobi Nobi seat is covered by JR pass fully. Please see the links below to learn more:
Rapid Moonlight Nagara
This train is operated as a seasonal train. It usually runs in spring break, summer break and winter break. These periods are mostly same as Seishun 18 Kippu sales period.
Therefore the train is mostly packed by Seishun 18 Kippu holders. Please see the link below to find more information about Moonlight Nagara.
Rapid Moonlight Shinshu 81
This is another seasonal train. It usually runs in same period as Moonlight Nagara. But in most of season, the number of trips is smaller than Moonlight Nagara. This train runs from Shinjuku to Matsumoto. There is no trains to Shinjuku from Matsumoto.
Reservation for overnight train
Actually this is a big issue. There is no online booking available. You have to book a seat after you arrive in Japan. That means you may not be able to get a space. You must have a back up plan if you use overnight train in your trip plan.