Temperatures throughout the country start to rise in March, after the cold winter. While northern parts of Japan (Hokkaido, Tohoku) are still cold, they're less cold than in January or February.
In Sapporo, capital of Hokkaido, expect average highs of 39° F (4° C) and lows of 25° F (-4° C). The major cities on Honshu and Kyushu (Tokyo, Osaka, Kyoto, Fukuoka) experience warmer daytime temperatures, especially as the month progresses. Average March highs in these cities sit at around 57° F (14° C), with lows of 41° F (5° C). Sub-tropical and tropical Okinawa is even warmer, with average highs in Naha of 70° F (21° C) and lows of 61° F (16° C).
Japan's wet season throughout the country is the summer, so rainfall remains low in March. In Hokkaido and on the Sea of Japan Coast of Honshu, there is still quite a lot of snowfall in March, though. That's because the Sea of Japan coast gets the brunt of the cold winter weather coming off Siberia and China, which the east coast of Japan is shielded from by mountains.
Japan's famous hanami, or cherry-blossom-viewing parties, begin in some parts of the country (such as Kyushu) in mid-late March. The exact date varies from year-to-year as temperatures aren't always uniform. Sunnier late-March weather can be conducive to sitting outside, in the shade of a cherry tree, and celebrating with some Nihonshu. But, be warned if you're continuing the celebration after dark that evening temperatures are likely to still be cold.
Crowds and Costs
March is shoulder season in Japan. More visitors come than in the colder months of December-February, but not as many as in the 'proper' spring months of April and May.
Japanese schools take a couple of weeks' holiday later in March, so expect a lot of places to be very busy. The Japanese like to get out and about and enjoy their own country, whether that's at amusement parks or at cherry-blossom parties, so even when there aren't so many foreign travelers around, you may be competing for space with locals.
Ski season continues into March. While not so many foreign travelers come to Japan to ski, this is a popular activity with locals. Expect high-season accommodation prices at places around ski fields, which are mostly around Nagano, Niigata, and Hokkaido.
Where to Go
Southern parts of the country are, in general, warmer in March. If this is important to you, make Tokyo the furthest north you venture. Kyoto and Hiroshima are highlights of western Honshu, and temperatures will be comfortable for outdoor sightseeing in March. Kyushu can also be really pleasant at this time of year, and tends to be a few degrees warmer than most parts of Honshu. Highlights of Kyushu are the cities of Nagasaki and Kumamoto, and the natural volcanic attractions around Mt. Aso and Beppu.
Although March isn't peak season in Okinawa (that's the summer), it's a nice time to go. It may be too cool to swim in some places, but parts of the island chain are tropical.
On the other end of the spectrum, if you enjoy snow sports, head to the mountains around Nagano and Niigata, on the Sea of Japan coast of Honshu. Snow lingers here for quite a while, especially in the mountains.
What to Do
It would be a mistake to travel to Japan in March and not seek out a hanami (in fact, you probably won't need to seek one out, as they will be obvious!). The Japanese are fanatical about their flowers, and the delicate pink sakura flower is a symbol of the country. At hanamis, people set out rugs or tarpaulins beneath the trees in parks and temples and celebrate the spring with food and drink (in Japan, there's always a lot of drink!). More southern parts of the country, such as Kyushu and western Honshu, may see their first sakura blooms in mid-March, followed by a 'wave' up the country into April.
Aside from hanami, March is a good time to enjoy general sightseeing activities in most parts of Japan. It's usually warm enough to get outside, but not too warm. Combine indoor activities like museums and galleries with outdoor activities when weather permits. Temples and shrines around the country offer the best of both worlds, as they usually have beautiful indoor spaces to check out, as well as well-maintained grounds for an outdoor stroll.
Hanami—cherry blossom viewing parties. Cherry trees bloom from mid-March, sweeping up the country into April. Cherry blossom viewing parties are a favorite annual pastime of many Japanese, from kids to suited businessmen.
AnimeJapan, Tokyo. If you're into anime, you won't want to miss AnimeJapan, one of the largest anime events in the country. It's usually held for a few days in late March.
Hinamatsuri. Every year on March 3rd, homes, shrines, and other public areas are decorated with traditionally-dressed dolls, celebrating Girls' Day.
Traveling to Japan in March? Check out these great itineraries
Classic Highlights of Japan - 14 Days. On this two-week journey to the four corners of Japan's main island, Honshu, you'll have plenty of time to enjoy its unmissable attractions. You'll visit sacred temples and shrines, go bike riding through the countryside, and roam around the capital's most famous neighborhoods.
Cities & Islands of Japan: Tokyo, Osaka, Nagasaki, & More - 10 Days. This 10-day trip will take you to Tokyo and Osaka, as well as some of the lesser known islands surrounding the main islands. Star gaze on Hachijojima, check out the volcano within a volcano on Aogashima, and more.
Explore Japan: Tokyo, Nikko, Hakone, & Kyoto - 10 Days. Along with two major cities–modern Tokyo and traditional Kyoto–this itinerary also takes you to the beautiful mountainside areas of Nikko and Hakone. A mixture of old-meets-new Japan, this trip has all you need to experience multiple sides of the country.