In 1684 the Qing court dispatched governor Zhou Chang and local official Jiang Yuying to rebuild the temple, renaming it Xianshi Temple. The following year, the Taiwan Provincial Academy was established in the temple, and from then until the beginning of the Japanese occupation of Taiwan this school was regarded by Taiwanese as the most prestigious one on the island.
清廷所派的巡道周昌與知府蔣毓英於隔年予以整修，改名為「先師廟」，並於清康熙二十四年（1685）將「台灣府儒學」（簡稱台灣府學）設立於此。