Weather-wise, spring and autumn are probably the best times to visit Kyoto, although they're also popular times for tourists and school groups. Having said that, although the summers (June-Aug) can be muggy, it's still a nice time to be there. If you're really out to avoid crowds, winter (Dec-Feb) - though very cold - might be just your ticket. Holidays and festivals are celebrated with crowded gusto in Kyoto, so cherry-blossom season in April and Golden Week (late April/early May) are great times to be in the city.
There's no question that the most appealing seasons in Kyoto are spring and autumn. Summers are too muggy; the surrounding mountains keep the air from moving around, making things stifled and sticky and producing ample rain. Winter is cold but not devastatingly so, and aesthetically speaking it's quite pretty. However, spring cherry blossoms and autumn amber leaves are just too good to miss.
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