Japan have markedly four seasons, and each with gradients in between. The spring stats with the plum blossoms and ends with the cherry blossoms. The summer contains the rainy season, even though you can catch almost guaranteed sun on late May/early June and - if you are lucky - late August. The Autumn stretches over 2 and a half months moving along the country spreading multiple colors, and of course, the winter can be mild on the southern regions, or intense further north. If you are looking for any of the four seasons, Japan have you covered with the best scenery.
While the below image show the Tourist high seasons, it also serves to discern the Hanami (Spring) and Koyo (Autumn) seasons in March and November.
For those dreaming of catching a white Christmas, it is important to notice that not all Japan is covered in Snow on late December. In fact, Tokyo seldom have a white Christmas (which makes it that much special when it happens). Snow is pretty much guaranteed anywhere in Chubu and Kanto region and up north during late December all the way to late February, and Ski resorts are aplenty, not to mention hot onsens ready to make your chilly body relax. A word of advice: book your onsens early, for you will be competing with Japanese internal Tourism for the spots.
Without a doubt the most celebrated season in Japan, with the world-famous Cherry Blossoms in late march covering most cities in white and pink cherry flowers. But the plum blossoms, that start a few weeks earlier and, depending on species, go all the way to mid April, will also add the extra feeling. With mild weather and incredible beauty, the Hanami is also the most coveted time of the year, and most cost/benefit stays are booked 3 or more months in advance, so plan ahead! Unfortunately, don't expect much privacy: Japan is literally invaded in late March, mostly by southeast Asians, and recently Chinese, so you better get used for intense crowds. But ... it is worth it.
The summer is not particularly the strong season of Japan due to the strong rainy season in between. Some areas, like Okinawa, might get less rain but one shouldn't be surprised by cloudy and rainy day - or even summer thunderstorms. That being said, it is still an amazing season and for those who don't care to get a little wet some days, it is a perfect time: pretty and low-season, what more do you want? Just be ready for indoors activities.
The second most celebrated time, after Hamani of course, The famous Autumn colors cover the whole country during more than 2 month, slowly moving from southwest to northeast. Depending on the time of the year, you can catch the trees starting or ending the color change. To better grasp this incredible season, check Japan-guide's map for autumn colors ↗. One of the benefits of this spread out season is that despite pretty, tourists don't clump on the same week like in the spring, so it is usually less crowded.
Typhoon Season Warning
Keep in mind that the Typhoon Season can hamper your travel plans. The Typhoon Season happens between August and September, though officially the season lasts from late May to early November. If you are going to Japan in August/September, be on the ready for delayed flights due to weather. Read more about it here