Quick Answer
Late March to mid-April (cherry blossoms) and mid-November to early December (autumn foliage) are Japan's most magical seasons. But they're also the busiest and priciest. For better value with great weather, visit May-June (before rainy season) or October (warm, clear, uncrowded).
Cherry Blossom Season (Late March–Mid April)
Sakura season is Japan's crown jewel. Blossoms open in Kyushu first (late March), reach Tokyo and Kyoto by early April, and arrive in Hokkaido by early May. The bloom lasts only 7-10 days per location. Track forecasts on japan-guide.com — timing varies by 1-2 weeks each year. Expect peak hotel prices (2-3x normal) and fully booked ryokans. Book 3-6 months ahead for Kyoto.
Summer (June–August)
June brings tsuyu (rainy season) to most of Japan except Hokkaido — humid and wet. July-August is hot (35°C+) and humid, but it's matsuri (festival) season: Gion Matsuri in Kyoto (July), fireworks festivals nationwide, Obon dance festivals. Hokkaido is the escape — pleasant 20-25°C with lavender fields in Furano. Summer is actually a great time if you head north.
Autumn Foliage (October–December)
Japan's autumn colours rival New England. Foliage peaks in Hokkaido (October), reaches Tokyo and Kyoto (mid-November to early December), and lingers in Kyushu through December. Temperatures are comfortable (15-22°C), skies are clear, and crowds are smaller than cherry blossom season. This is many Japan veterans' preferred season.
Winter (December–March)
Ski season in Niseko, Hakuba, and Nozawa Onsen brings world-famous powder snow (January-February). Cities are cold but manageable (0-8°C). Winter illuminations transform Tokyo and Osaka. Hot spring (onsen) culture peaks — nothing beats an outdoor rotenburo in falling snow. Flights and accommodation are cheapest in January-February (excluding New Year).
Budget Tips
The Japan Rail Pass (7/14/21 days) pays for itself in 2-3 shinkansen rides. Avoid Golden Week (late April-early May) — the entire country travels and prices spike. Budget hotels in Tokyo and Osaka are surprisingly affordable ($40-60/night) if you book capsule hotels or business hotels. Convenience store meals (7-Eleven, Lawson) are genuinely excellent and save ¥1,000+ per meal versus restaurants.