The Confucius Temple of Taipei can trace its origins back to 1875 when the Qing court established Taipei as a prefecture City for Northern Taiwan. In 1879, construction began in Taipei City, including the literary and martial temples which were to be built inside the southern gate of the city. Both temples faced south, with the Literary Temple on the left and the Martial Temple on the right.

Taiwan military commissioner Xia Xian Lun(夏獻綸) and Taipei prefect Chen Xing Ju(陳星聚) oversaw the construction of the Taipei Confucius Temple. In 1881 the Da Cheng Temple, Yi Gate and Chong Sheng Shrine were finished. In the second year, the gentry of Taipei suggested asking for donations, and work began on the Li Gate, the Yi Path, the Ling Xing Gate, the Pangong Pond and the Wan Rengon Wall. The magnificent Taipei Confucius Temple was finally completed in 1884.

During the time when Liu Ming-chuan(劉銘傳) was the governor of Taiwan, every year the temple would hold a major ceremony, an important event for the literati. In 1891, after Shao You Lian was appointed as governor, additional ceremonial objects were imported from Fu Jian, and musicians and performers who understood the rites were hired to come to Taipei to teach.

However, in 1894,  war broke out between China and Japan, and Taiwan was ceded to the Japanese. The following year, Japanese troops occupied Taiwan and the period of Japanese occupation began. During the first few years of Japanese occupation, resistance was strong; the Japanese military occupied the Taipei Confucius Temple,  damaged and destroyed most of the memorial tablets of Confucius and other ancient saints and sages. Many of the ceremonial objects and musical instruments were also lost, and the buildings gradually fell into a state of disrepair and the Confucius ceremonies ceased.

In 1907, the Japanese tore down the temple to build the Taipei First Girls High School. Not long after, they built a pavilion within the Japanese school, and put inside it the carved memorial tablets of Confucius and other ancient saints and sages. Every year on Confucius' birthday, the pavilion would be opened up so that the students and teachers at the school could worship.
 
In January 1917, the Ocean Society of Poets and the Da Zheng Association organized the Chong Sheng Society. Japanese Kimura Tadashi was made President, and two members of the Taipei gentry, Yen Yun-nien and Li Ching-sheng, were made Vice Presidents. Every year, on Confucius's birthday (the 27th day of the eighth month of the lunar calendar) the tablets were respectfully taken out of the pavilion of the Japanese school and sent to the Tataocheng Public school, the Penglai Public school, the Lungshan Temple at Mengchia or the Paoan Temple at Da Longdong for worship ceremonies to be held. Although the organizers of these ceremonies wanted to rebuild the Confucius Temple, their wish could not be realized because of the lack of money.