If you're flexible, try and avoid going during busy travel seasons (winter holidays & summer are the busiest and most expensive). (ordinarytraveler.com)
With the upcoming busy travel season, what are the best ways of traveling with your best friend? (rivertrailahandpetlodge.com)
Especially busy travel seasons for Japanese domestically are New Year's, end of April / early May between school years, July and August is school holidays, so masses of college students and high school students on school trips horde long distance trains and famous Japanese sites like Kyoto's temples. (ordinarytraveler.com)