It was originally built in 1111 during the Northern Song dynasty; the neo-Confucian scholar Yang Shi (楊時) taught there, but the academy later fell into disuse and disrepair.

Yang Shi visited the Donglin Temple and felt that it was a good place for teaching.

When he finished his scholarship, he travelled to Wuxi and saw that the layout of the academy was similar to the Donglin Temple, so he taught at that site for 18 years.

In 1604, during the Wanli era of the Ming dynasty, Gu Xiancheng (1550–1612), a Grand Secretary, along with the scholars Gao Panlong (高攀龍; 1562–1626), Qian Yiben (錢一本), An Xifan (安希范; 1564–1621) and Yu Kongjian (余孔兼) restored the Donglin Academy with financial backing from the local gentry and officials such as Ouyang Dongfeng (歐陽東風), the governor of Changzhou, and Lin Zai (林宰), the county magistrate of Wuxi.

The contemporary academy was a reconstruction during the Qing dynasty by the Yongzheng and Qianlong emperors to win the support of Han Chinese scholars living in Wuxi.