Map from Google - Japan

The climate of Japan is cold in the north (where snow and ice dominate in winter), temperate in central regions, and almost tropical in the small southern islands. The rains are abundant almost everywhere, and between summer and autumn the country is hit by torrential rains and typhoons.
The climate of Japan is influenced by monsoons: in winter it's dominated by cold currents from the north-west, while in summer the wet and humid currents of tropical origin prevail.

Japan is a large archipelago, consisting of more than 3,000 islands and islets, and is very extended in latitude: Hokkaido, the northernmost of the main islands, touches the 45th parallel north (the same latitude as Montréal, Canada), Tokyo, the capital, is located on the 36th parallel (the same latitude as Nashville, TN), the southern part of the island of Kyushu touches the 31th parallel (the latitude of the Austin, TX), and finally the small southern islands (Ogasawara and Ryukyu) reach tropical latitudes (Yaeyama, the southernmost of the Ryukyu Islands, are located just north of the Tropic of Cancer, the same latitude of Miami, FL).
The sea temper the climate while increasing moisture, but the influence of the great Asian continent, mountain ranges (which cover three quarters of the country) and ocean currents (the north-eastern sea is crossed by the cold current called Oya-Shio, while the southern sea is crossed by the warm current called Kuro-Shio), as well as the latitude, tend to accentuate the differences between seasons and between different areas.

Two common features of the climate of Japan are the lack of a real dry season and the high summer rainfall amount.
Overall, the rainiest areas, where over 2,000 millimetres (79 inches) per year fall, are, on the island of Honshu, the central-western part (where rainfall is abundant even in winter, because of the north-west monsoon), the Kii Peninsula (where instead the effects of the summer monsoon is more pronounced), and also the entire island of Shikoku and the central-southern part of Kyushu (equally affected by the summer monsoon).
The least rainy area is the northernmost island of Hokkaido, where, because of the cold winter and the reduced influence of the summer monsoon, the annual rainfall drops below 1,000 mm (40 in).

Winter is very cold on the island of Hokkaido, where the cold winds from Siberia cause freezing temperatures, and the slopes exposed to the north-west experience also heavy snowfall. The eastern area of the island is a bit drier. The cold current of the Sea of Okhotsk even push ice floes to the north coast of the island.
In Sapporo, which has hosted the 1972 Winter Olympic Games, the average temperature in January is -4 degrees Celsius (25 °F), the temperature remains below freezing (0 °C or 32 °F) from December to March, and there are on average 130 days with snow in a normal winter season. In February, the Sapporo Snow Festival is held, attracting millions of visitors to admire statues and sculptures made of ice.
Here are the average temperatures of Sapporo.
Average temperatures - Sapporo
Min (°C)-7-7-3381317191481-4
Max (°C)-1041217222526221682
Min (°F)191927374655636657463425
Max (°F)303239546372777972614636

In Sapporo, 1,100 mm (43 in) of rain or snow per year fall; the (relatively) least rainy season is spring. In winter, frequent snowfalls occur. Here is the average precipitation.
Average precipitation - Sapporo
Prec. (mm)1159580555545801251351101051101105

The sea at Sapporo is very cold in winter (but in the north-eastern coast it's even colder), and stays cool in summer, even though it reaches 21 °C (70 °F) in August.
Sea temperature - Sapporo
Sea (°C)645691318212016128
Sea (°F)433941434855647068615446

In the interior of Hokkaido, the average in January drops down to -10 °C (14 °F).

Sapporo snow festival

In the northern tip of the island of Honshu, winter is still cold, with averages of -3/-2 °C (27/28 °F) in January and February, and epic snowfalls on the north and north-west slopes, directly exposed to the prevailing wind; moving south, in the north-central part of the island (see Niigata), the average rises to 2/3 °C (36/37 °F), but winter is still cold enough to cause frequent snowfalls on the western side, which in this season is definitely more humid than the eastern side, because the prevailing winds coming from Siberia, initially dry, pick up moisture from the Sea of Japan, and drop it on the north-west side, while the other side is protected by the mountains which form the backbone of the country.
Average temperatures - Niigata
Min (°C)002713182223191373
Max (°C)661016212428312620149
Min (°F)323236455564727366554537
Max (°F)434350617075828879685748

In Niigata, precipitation is abundant: even 1,800 mm (70 in) annually. In winter, with the temperature slightly above freezing and the wind coming from the sea, it rains and snows almost every day. Here is the average precipitation.
Average precipitation - Niigata
Prec. (mm)195125120100951251901051751651702651830

At Niigata, the sea becomes warm enough for swimming in August and September, while it is a bit cool in July and October.
Sea temperature - Niigata
Sea (°C)1188101317212423201713
Sea (°F)524646505563707573686355

While on the western side the winter is very annoying, with leaden skies, rain and snow falling almost daily, and with possible sea storms, the eastern side is instead protected by mountain ranges, so it experiences a fair number of sunny days. In Tokyo and Osaka, winter is the sunniest and driest season of the year; the temperatures are quite cold, with maxima around 8/10 °C (46/50 °F), and minima around freezing, but it's bearable. Snowfalls in the capital are quite rare, even more so in the southern conurbation of Osaka-Kobe-Kyoto, and in general along the south-facing shores of the Seto Inland Sea, protected as they are by the mountains.
Average temperatures - Tokyo
Min (°C)124914182223201484
Max (°C)101014192326293127221612
Min (°F)343639485764727368574639
Max (°F)505057667379848881726154

In Tokyo, 1,500 mm (60 in) of rain per year fall; lying on the eastern side, it is protected from the winter monsoon, so here the winter is definitely the driest season, while in the other seasons it rains a lot, with a maximum in September and October. Here is the average precipitation.
Average precipitation - Tokyo
Prec. (mm)505512012514017015517021020095501530

At Tokyo, the sea is much warmer in winter, and it becomes warm enough for swimming from July to October, and a bit cool but still acceptable in June.
Sea temperature - Tokyo
Sea (°C)171616172022242625232119
Sea (°F)636161636872757977737066

In the mountainous areas of Japan, culminating in the 3,778 metres high Mount Fuji, winter temperatures are naturally lower, and the snow is abundant, especially on the western slopes. On the island of Honshu, there are famous ski resorts such as Morioka, in the far north, and Nagano, northwest of Tokyo, the site of the 1998 Winter Olympics.
Here, for example, average temperatures in Karuizawa, a resort town at 1,000 meters of altitude, in the prefecture of Nagano, northwest of Tokyo, where the inhabitants of the capital go in the summer to escape the heat.
Average temperatures - Karuizawa
Min (°C)-10-9-605111516124-1-6
Max (°C)22613182124262015105
Min (°F)141621324152596154393021
Max (°F)363643556470757968595041

In some mountainous areas, such as Mount Zao, there is the curious phenomenon of the "snow monsters" due to moisture carried by the wind, which accumulates in the form of ice on the trees.

Monsters of snow on Mount Zao

On the island of Kyushu, the winter climate is relatively mild, but quite rainy. In January, the average goes from 4/5 °C (39/41 °F) on the north coast, to 7/8 °C (45/46 °F) of the southern coast.
On the southernmost islands (see Ishigaki, Okinawa), winter is so mild as to remind autumn or spring, even though the rains are abundant. In Okinawa, where the climate is almost tropical, the average in January is around 17 °C (63 °F). Here it never freezes or snows (see Naha).
Average temperatures - Naha
Min (°C)151516192225272726232016
Max (°C)202022242729323230282521
Min (°F)595961667277818179736861
Max (°F)686872758184909086827770

In Okinawa, 2,000 mm (79 in) of rain per year fall, with a maximum from May to September (but in which there is a relative break in July), and a relative minimum in winter, when still about 100 mm (4 in) of rain per month fall. Here is the average precipitation.
Average precipitation - Naha
Prec. (mm)1051201601652302451402402601551101052040

The sea in Okinawa is never cold, so that the temperature drops to 22 °C (72 °F) in February and March, while it becomes very warm in summer.
Sea temperature - Naha
Sea (°C)232222242527292928272524
Sea (°F)737272757781848482817775

Spring, which is rainy throughout Japan, arrives quite early in Tokyo and the eastern and southern slopes of Honshu, while moving north, it arrives progressively later.
A good indication of the arrival of spring is the blooming of the cherry trees (hanami): in Tokyo and Osaka the full bloom occurs around March the 30th, in Sendai around April the 15th, in Sapporo around May the 5th, in Okinawa even around February the 1st. The flowering tends to last longer in the south than in the north (about two weeks in the south, one in Hokkaido, and even a month in Okinawa), and the date can vary from a few days to one week before or after, depending on year.
A good time to visit Japan is the month of May (which in the north of the country is also the driest month of the year), and also the first part of June, because it's acceptable almost everywhere (but in the Ryukyus it's already hot), before the muggy heat and the rains that are typical of summer.

Cherry blossom in Japan

Summer, which begins in mid-June, is hot and muggy in much of the country, save only in Hokkaido and the northern part of Honshu, which typically have more pleasant temperatures. August is the hottest month in the main islands, while in the small southern islands there are no differences between July and August. In August, the daily average temperature is around 20 °C (68 °F) in Hokkaido, 22/23 °C (72/73 °F) in the north of Honshu, and 26 °C (79 °F) in the area of Tokyo.
The heat is hardly bearable in Tokyo, Osaka and in the big southern cities of Honshu and Kyushu, also because of the so called "urban heat island" effect. In the hottest periods, minimum temperatures around 25/27 °C (77/81 °F) are not uncommon.
In most of Japan, summer is the rainiest season of the year. Particularly rainy is the west coast of Kyushu (see Nagasaki, Kagoshima): in some areas, even in the plains, 450 millimetres in a month fall! Here is the average precipitation in Kagoshima.
Average precipitation - Kagoshima
Prec. (mm)8011018020522045032022521010090702265

Here are the average temperatures in Kagoshima.
Average temperatures - Kagoshima
Min (°C)56813172125262318127
Max (°C)131417222528323230252015
Min (°F)414346556370777973645445
Max (°F)555763727782909086776859

In this southern part of the main islands of Japan, the sea is never cold, but it gets cool in the winter, when the temperature drops to 19 °C (66 °F) in February.
Sea temperature - Kagoshima
Sea (°C)201920212325272828262422
Sea (°F)686668707377818282797572

The southern coast of Shikoku is much more rainy than the northern one. In Hokkaido and northern Honshu, the rainiest months are August and September, in which from 100 to 200 mm (4 to 8 in) per month fall.
The rainiest periods are two: the rainy season begins with the "Baiu" or "plum rain" (June 15-July 15), which brings heavy rains, essential for the rice cultivation, especially in the south (where June is the rainiest month of the year).
In the second part of summer, starting from August, the typhoons, tropical cyclones coming from the south-west, begin to show up; they affect mainly the southern part of the country, but they may also affect Tokyo. The most intense typhoons can bring gale force winds and torrential rains, causing extensive damage.
The area of Osaka and Kyoto is relatively sheltered from typhoons, being surrounded by mountains.
Typhoons normally hit Japan in August and September, but they can do it for a longer period, from June to mid-October. The most affected areas are usually the smaller southern islands, and among the main islands, the south of Honshu and Shikoku, and the entire Kyushu.

In autumn, September is still hot and humid, at least in the south-central, and in Tokyo it is the rainiest month of the year. Even in Sapporo, September is the rainiest month, but here at this time the summer is already over. Instead, the southern Okinawa is still in the midsummer.

Maple trees in autumn near a temple

In autumn, the woods and the trees surrounding the temples take on beautiful colors: the period in which you can go in search of trees (momijigari), especially maples, which turn red, varies depending on area: in Hokkaido it goes from late September to late October (but already in mid-September in inland mountainous areas), in the north of Honshu from October to early November, in Nikko and in the lake Chuzenji area from early October to mid-November, in south-central Japan and in Kyoto from mid-November to early December.

When to go

Cold, heat, rains and typhoons characterize the climate of the various areas of Japan, so it is difficult to find a good time for all the country. However, the best time to visit Japan is spring, from April to early June; you can choose in particular the month of May, or follow the cherry blossoms, which as mentioned vary from area to area. In May, the maximum temperatures are around 17 °C (63 °F) in Sapporo, 23 °C (73 °F) in Tokyo, and 26.5 °C (79.5 °F) in Okinawa. April may still be cold on the island of Hokkaido.
Winter is freezing cold in the north, while it is mild and rainy in the south. Summer is hot and humid almost all over the country, with the risk of typhoons and torrential rains. Autumn is rainier than spring, and still has the risk of typhoons in the first part, at least until the middle of October. It should be remembered, however, that even the spring is a rainy season, especially in the south.
Wanting to go in autumn, you can choose the period mid-October to mid-November, by which time the risk of typhoons should be over, and the heat in the south, or you can choose the period of the fall foliage. In October, the temperatures are already cool in Sapporo, while they are pleasant in the rest of Japan, the humidity has decreased and the rains are less abundant. In November, it gets cold on the island of Hokkaido, but in the rest of the country the temperature is still mild.
Wanting to go to in winter, for example at New Year, you can choose the most sheltered and sunny area of Honshu (Tokyo, Osaka, Kyoto), or the southernmost area of the main islands and the tropical one (Kagoshima, Okinawa).
To visit the main cities in the summer, August is partly preferable to July, having more sunshine and less rainfall, but it is also true that it is even hotter and has a greater risk of typhoons.
Being rainy and not very sunny in summer, Japan is not the best country for swimming and sun bathing. Anyway, as we have seen, the sea is a bit cool even in this season in Hokkaido, while it's quite warm, with a temperature equal or greater than 23 °C (73 °F), for most of the year in Okinawa, from July to October in Tokyo and Yokohama, and in August and September in Niigata. In Okinawa, the best month for a beach holiday is July, because it experiences a pause between the two rainy periods (May-June and August-September), although showers in afternoon are possible, in addition to the passage of tropical storms and typhoons.

What to pack

In winter: in Hokkaido and northern Honshu, up to Niigata and Fukushima, very warm clothes, synthetic thermal long underwear especially for Hokkaido, fleece, down jacket, gloves, scarf, hat, raincoat.
For the area of Tokyo, Kyoto and Osaka, warm clothes, sweater, jacket, hat, possibly a raincoat or umbrella.
For Okinawa and the southern islands, spring/autumn clothes, sweatshirt or sweater, jacket, raincoat or umbrella.

In summer: in northern Hokkaido, spring/autumn clothes, light for the day, a sweater and a raincoat. In Sapporo and northern Honshu, light clothing, a sweatshirt and a light jacket, raincoat or umbrella.
Throughout south-central Japan and the islands, including Okinawa and Tokyo, light, tropics-friendly clothing, a scarf for the breeze, light sweatshirt for the evening and air conditioned places, light raincoat or umbrella. For mountainous areas, warmer clothes depending on altitude, spring/autumn clothes at about 2,000 metres (6,500 feet) in Honshu.
For the reef, equipment for snorkeling, water shoes or rubber soled shoes.
In homes and temples, it is customary to remove shoes before entering: it can be useful to wear shoes without laces, or at least easy to take off.