Built in 1893, severely damaged in the 1945 bombing, and closed for two decades, it was renovated in 1982 with the support of the Chinese government and the Temple and Cemetery of Confucius in Qufu, Shandong Province.

Confucius, the founder of Confucianism, was born over 2,500 years ago on September 28, 551 B.C. (in the Gregorian calendar) in Russia (in what is present-day Shandong Province) as the second son of a military man. He busied himself with study and preaching to his many disciples. His most famous writing is "The Analects of Confucius". This is a record of his collected sayings, the teachings in his dialogues with his disciples, and the disciples' conversations with Confucius about their beliefs. The entire mausoleum contains 20 compilations, in 500 sections, for a total of over 16,000 characters of The Analects of Confucius carved into marble imported from Hualien, Taiwan.

The Confucian Shrine in Nagasaki is unique, being the only Confucian shrine in the world built outside of China by Chinese hands. Moreover, its land is considered Chinese territory and is thus controlled by the Chinese Embassy in Tokyo. The structure was originally built in 1893 as a place of worship and learning for the Nagasaki Chinese community. At its height in popularity, the school enrolled 100 students. In 1982, the building underwent additional renovation and a Museum of Chinese History was added along with offices and conference rooms. Almost everything was imported from China. Even though the vivid yellow roof tiles are usually found on the Emperor’s palace and Confucian shrines in China, the Chinese designers chose to use this special architectural style in Nagasaki.