Japan is a temperate region with, more or less, four seasons (some believe the rainy season should be a fifth season), but because of its great length from north to south, its climate varies from region to region: the far north is very cold in the winter, while the far south is subtropical. The climate is also affected by the seasonal winds blown from the continent to the ocean in winters and vice versa in summers. The waters of the Kuroshio Current also warm the Pacific side of Japan, sustaining the coral reefs of Japan, the northernmost coral reefs in the world. Unfortunately, due to pollution, these reefs are now dying.

Late June and early July are a rainy season (except in Hokkaido), as a seasonal rain front or baiu zensen (????) stays above Japan. In the late summer and early autumn, typhoons develop from tropical depressions generated near the equator, and track from the southwest to the northeast, often bringing heavy rain.

Japan's varied geographical features divide it into six principal climatic zones.

• Hokkaido: Hokkaido has a temperate climate with long, cold winters and cool summers. Precipitation is not heavy, but the islands usually develop deep snow banks in the winter.
• Sea of Japan: The northwest wind in the wintertime brings heavy snowfall. In summers, the region is cooler than the Pacific area, but it sometimes experiences extremely hot temperatures due to the Foehn wind phenomenon.
• Central Highlands (Chuo-kochi): A typical inland climate, with large temperature differences between summers and winters and between days and nights. Precipitation is light.
• Seto Inland Sea (Seto-naikai): The Mountains of the Chugoku and Shikoku regions block the seasonal winds, bringing mild weather throughout the year.
• Pacific Ocean: Experiences cold winters with little snowfall and hot, humid summers due to the southeast seasonal wind.
• Nansei-shoto (Ryukyu) or Southwest Islands: Has a subtropical climate with warm winters and hot summers. Precipitation is very heavy, especially during the rainy season. Typhoons are common; in 2004 a record number of 10 typhoons reached the main islands.