Ume (Asian plums) blossoms can be viewed from late January to March in Honshu region.
Sakura or cherry blossoms bloom in March and May on the mainland of Japan. Viewing pretty sakura flowers is a main reason for many travelers to visit Japan.
Japanese rainy season starts in early June and ends in middle July. If you don't like rain avoid this time of year. If you don't mind gloomy weather, it can be a cool and nice time to visit Japan. In Hokkaido, there is no rainy season, this is a good time to visit Hokkaido.
July and August are usually hot and humid on the mainland in Japan. If you are visiting Hokkaido, these months are the best, because the weather is cool and dry.
Obon (August 13-16) is another Japanese vacation season. If possible, avoid traveling during this time. However, Tokyo tends to be less crowded during obon since many people travel out of the city to their home towns.
Japan's fall foliage season begins in mid. October and extends through early December.
Winter (December - February)
Winter in Japan is cold, but it's not so bad. In Tokyo, the temperature hardly drops below 33F. January and February is a good time for skiing. There are many good ski resorts in Hokkaido and the north region on Honshu island. See Snow Resorts in Japan.
Colorful holiday illuminations and Christmas decorations can be seen around the country from November to December.
New Year's is an important holiday for Japanese people. Japanese airports, highways, and train stations are crowded during the last week of December and the first week of January. Try to avoid traveling this period of year.