There are scheduled national holiday periods that basically allow the whole country take a holiday simultaneously. So be forewarned, there is usually a mass exodus of travellers from the city to the country and then in the opposite direction. All trains, ferries, airline flights and accommodations, etc. will be close to capacity and reservations completely booked in these holiday periods.
Try to avoid traveling during the periods listed below:
New Year's Holidays
December 27 to January 4 and adjoining weekends.
Golden Week Holiday Season
Around April 29 to May 5 and adjoining weekends.
One week season around August 13 and 15.
Around September 23 for 4 or 5-days (A period of consecutive national holidays)
Also be aware of School Holidays: Winter Break
From the end of March through the beginning of April and from the end of July through August.
Approximately lasts for about 1 month, usually from mid June to mid July. The Typhoon season is in summer.
Three-day Consecutive Holidays
Some of Japan's National Holidays are varied each year so to make 3-day consecutive holidays and to encourage the tourism in Japan. For example, Marine day used to be fixed on 20.July, but it varies each year and it is on 17th of July in 2017, falls on Monday.