The Japan Rail Pass
will cover your base fare
on the night trains, but it will not cover the “limited express” fee or the lodging fee. In other words, your rail pass will give you a discount of around 10,000 to 20,000 yen. If you choose a normal seat or a bare minimum carpeted area, however, you may not need to pay a supplemental fee.
When purchasing your ticket, please ask the ticket agent for details, as these fees are subject to change.