Although archaeological evidence places the first human settlement on the islands of Japan at approximately 10,000 BC, relatively little is known about human activity in the area before the 6th century AD. During the 8th century, when the powerful Buddhist clergy became involved in the affairs of the Imperial government, the Emperor chose to relocate the capital to a region far from the Buddhist influence. Emperor Kammu selected the village of Uda, at
the time in the Kadono district of Yamashito Province, for this honor.

The new city, Heian-kyō (平安京 "tranquility and peace capital"), became the seat of Japan's imperial court in 794, beginning the Heian period of Japanese history. Later, the city was renamed Kyoto ("capital city"). Kyoto remained Japan's capital until the transfer of the government to Edo in 1868 at the time of the Imperial Restoration.

The city suffered extensive destruction in the Ōnin War of 1467-1477, and did not really recover until the mid-16th century. Although there was some consideration by the United States of targeting Kyoto with an atomic bomb at the end of World War II, in the end it was decided to remove the city from the list of targets due to the "beauty of the city."

As a result, Kyoto is the only large Japanese city that still has an
abundance of prewar buildings, such as the traditional townhouses known as machiya.

A common English pronunciation of Kyoto has three syllables as /key-oh-toe/ [kʰi'otəʊ]; however, the Japanese pronunciation has only two: [kʲoːto].

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