Nichinan has a Humid climate (Köppen Cfa) characterized by warm, wet summers and cold winters with heavy snowfall. The average annual temperature in Nichinan is . The average annual rainfall is with July as the wettest month. The temperatures are highest on average in August, at around , and lowest in January, at around . Its record high is , reached on 19 August 2020, and its record low is , reached on 16 February 2011.
