Japan's weather is very varied, and between Hokkaido in the north to the islands of Okinawa in the south, there's no uniformity in the weather in January. That being said, January is mid-winter and the coldest month throughout the country.
In Sapporo and other parts of Hokkaido, the northernmost island, visitors should expect very cold temperatures. Sapporo experiences an average January high of 30° F (-1° C) and a low of 17° F (-8° C). The larger cities of Honshu and Kyushu are considerably warmer, but some snow can still be expected in Tokyo, Osaka, and Kyoto in January. These three cities, as well as Fukuoka in Kyushu, experience average January highs of around 50° F (10° C), and lows of 36° F (2° C), though temperatures will be on the colder end when there's snow.
Further south, in the islands of Okinawa, winters are mild. Most of the island group is sub-tropical, while some are tropical. Naha, the capital of Okinawa, experiences January highs of 66° F (19° C), and lows of 57° F (14° C).
Rainfall is typically low in January, as when there is precipitation, it usually falls in the form of snow. Summer is the wet season in Japan.
An important feature of Japan's geography and climate to know about is that the mountains through the middle of Honshu shield the east coast from the worst winter weather coming off Siberia and China. So, although cities on the east like Tokyo can still experience cold temperatures in January, their winters are not nearly as harsh as those on the west.
Crowds and Costs
January is low season in Japan because of the colder temperatures, although its peak ski season in Hokkaido and central Honshu. While not so many international tourists come to Japan to ski, it's a popular activity with locals, so you can expect areas around ski fields to be busy in January.
Sapporo's annual Snow Festival often starts in late January, running into February, and this is a busy (and expensive) time to travel to Sapporo and Hokkaido. Book flights and accommodation as far in advance as possible if you want to attend this immensely popular event.
Although Okinawa experiences much warmer temperatures than much of the rest of Japan in January, this is not a peak time to travel there.
Other destinations of interest to travelers—such as Tokyo, Osaka, Kyoto, and Hiroshima—are not so busy with tourists in January, but these are big cities where there's always something going on, even during mid-winter. The season is no reason to avoid these places.
Where to Go
Where you go in Japan in January largely depends on what kinds of experiences you want to have. In general, the further south you go, the warmer the temperatures become, but aside from Okinawa, nowhere is warm in January.
If you enjoy snowy conditions, either for skiing or general sightseeing, then Hokkaido and Nagano are great destinations. In Hokkaido you can catch Sapporo's annual Snow Festival.
The major cities of Tokyo, Osaka, and Kyoto can be quite cold in January, but there are many indoor activities to enjoy there (galleries, museums, temples, theaters, restaurants...) that can be enjoyed in January. Kyoto in particular is an attractive city at any time of year, but a dusting of snow makes the hundreds of temples, shrines, and palaces even more pretty.
What to Do
The Japanese have got hot spring bathing down to a fine art, and while you can enjoy a soak in an onsen at any time of year, they're especially nice when the weather is cold outside. You'll find these all over the country, but it's worth spending a day or two in a dedicated onsen resort town such as Kurokawa Onsen (Kyushu) or Kusatsu (Gunma Prefecture).
If you enjoy skiing, visiting a Japanese ski resort can be fun. You'll mostly be surrounded by locals, as Japan isn't a major international ski destination. The largest concentration of ski resorts is in the Nagano area.
As mentioned above, general sightseeing in the major cities and surrounding areas is perfectly possible, and comfortable, in January. There are many indoor attractions to retreat to when it's cold out.
New Year. Japan takes a nationwide New Year holiday from 1-3 January. The Imperial Palace in Tokyo also opens its gates on 2nd January (it only does this twice a year) so visitors can take a look inside the grounds and even be greeted by the emperor waving from his balcony. It's extremely busy at this time.
Coming of Age Day. On the second Monday of January, young people who have turned 20 in the past year celebrate at shrines across Japan. Young women will wear attractive colorful kimono to attend shrines.
Sapporo Snow Festival. This famous festival featuring incredible ice sculptures is typically held in early February, although it sometimes begins later in January.
Traveling to Japan in January? 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.
Japan's Culinary Heritage - 11 Days. Eat your way through the Land of the Rising Sun on this immersive culinary tour. Get to know Japanese history and culture through its legendary cuisine, and treat your taste buds to everything from home-brewed sake to the freshest sushi, to delectable street food and a fancy gourmet feast.
Best of Tokyo & Kyoto - 7 Days. This week-long adventure splits its time between two of Japan's most important cities with a mix of customizable tours and free time to explore on your own.