Japan has a lot of rain — particularly during the rainy season (tsuyu, roughly mid-June through mid-July), during typhoon season (August–October), and in the form of regular showers throughout the year. Rain in Japan is not a disaster. Many indoor attractions are excellent, some outdoor experiences are actually better in rain, and the country's covered shopping arcade (shotengai) system means you can walk for kilometres without getting wet.
Indoor Attractions Worth Rainy Days
Tokyo
Tokyo National Museum (Ueno): The best all-day indoor destination in Tokyo — Japan's largest and most comprehensive museum. Even if you've already visited one gallery, another is always worth exploring on a wet afternoon.
teamLab Planets or Borderless: Entirely indoors, and the dark immersive environments are unaffected by outside weather.
Akihabara: Multiple storeys of indoor shopping, gaming, and entertainment. Hours can disappear in the Yodobashi building alone.
Department store basement floors (depachika): Isetan Shinjuku or Takashimaya's basement food halls are world-class food experiences entirely under cover.
Mori Art Museum: 53rd-floor contemporary art with rain on the floor-to-ceiling windows enhancing rather than diminishing the experience.
Kyoto
Kyoto National Museum: Excellent permanent collection of Japanese art and craft, enhanced by rotating special exhibitions. Consistently underrated.
Machiya cafes: Kyoto's converted townhouse cafes are designed for sitting and lingering. Rain provides the perfect excuse.
Nishiki Market: Entirely covered, with enough stalls and food samples to fill 2 hours.
Osaka
Osaka Museum of History: An excellent museum in a striking modern building overlooking Osaka Castle, covering the city's history from ancient times to the present. Entry ¥600.
Umeda Sky Building: The observation deck is partially outdoor, but the building itself and the underground "Takimi-koji" retro food hall are entirely covered.
Experiences Better in Rain
Moss gardens are most vivid after rain — Saihoji Temple in Kyoto (the "Moss Temple," requires advance reservation) reaches peak colour when wet. Temple rock gardens (Ryoan-ji, Daisen-in) have a different quality in rain — the water darkens the stones and empties the grounds of casual visitors. Rain in Gion on the lantern-lit Hanamikoji Street in the evening is cinematically beautiful. Japanese covered arcades (shotengai) are designed precisely for rainy weather — the shotengai in Kyoto, Osaka, and Kochi Prefecture are worth exploring in their own right.
Practical Rain Tips
Buy a kasa (umbrella) from a convenience store at the first sign of rain — they cost ¥500–¥700 and are practical rather than elegant. Japan sells excellent compact umbrellas; buying one locally saves pack space. Many temples provide plastic bag dispensers at the entrance for umbrellas — use them rather than dripping on tatami. Rain boots are available in specific outdoor shops if you're going to be doing significant outdoor walking.