A countrywide Japan Rail Pass is valid for 7, 14 or 21 consecutive days, a duration you choose according to your plans, when ordering a JR Pass. It is not possible to dispatch or split the validity period of a JR Pass.
A JR pass is valid per calendar day: it starts at 00:01 a.m. on the day of activation (even if you activate it later on the same day) and ends at 11:59 p.m. on the last day of the validity period. For example, from April 1 to 7 included, whatever the hour you first used it was.
Therefore, you should cleverly plan cleverly the hour of activation, so as not to “lose” a day of JR Pass use.
The train departure time is what is taken into account to decide if your trip is included in the validity period. You can then take a train very late on the last day, even if the trip lasts on the following day.
The JR Pass is valid even on the days you are not using it.
Some regional JR Passes offer different validity periods, which must be checked for each type of pass.