Kinkakuji was built in 1393 as a retirement villa for Shogun Yoshimitsu Ashikaga (1358-1409), who quit politics the following year to manage the affairs of state through the new shogun, his 10-year-old son.

The beauty of the shogun's pavilion makes it difficult to imagine the era in which he lived out his retirement: the country was in turmoil and Kyoto residents suffered severe famines and plagues — local death tolls sometimes reached 1,000 a day.

After his death, his son converted the building into a Zen temple of the Rinzai school, in accordance with Ashikaga's wishes.

It is a three storey temple, each being build and decorated with a different style.
The ground floor is surrounded by a balustrade above the pound Kyoho-Chi, and the rooms are designed as a palace, in the so called Shinden-zukuri style.
The fisrt floor is built as a samurai house, when the second floor is similar to Zen 's Temple.

The temple was burned down several times during the Onin War. In 1950, the Golden Pavilion was again burned down, this time by a fanatical monk. A fictionalized version of the events is at the center of Yukio Mishima's 1956 novel Kinkakuji (The Temple of the Golden Pavilion). The reason given for this fanatical move, is a revolt against the materialism of the modern Japan represented by the Temple covered of gold leaves and with a sophisticated design not in line with the minimalism of the Zen influence.

The present structure dates from 1955, which is true to the original except that both upper stories are covered in gold leaf, in accordance with Ashikaga's original intentions.