Towards the late Edo period, one of the most important educational institutions of the shogunate, the Shōhei-zaka Gakumonjo (昌平坂学問所)), or Shōheikō (昌平黌), was founded on its grounds.

The first structure, the Sensei-den (先聖殿), constructed by the neo-Confucian scholar Hayashi Razan (1583–1657) in his grounds at Shinobu-ga-oka (now in Ueno Park).

The school was known as the Shōhei-zaka Gakumonjo (昌平坂学問所) or Shōheikō (昌平黌), after the supposed birthplace area of Confucius (昌平, Shōhei in Japanese).

The academy covered a much larger area than the current grounds of the temple, including where the modern Tokyo Medical and Dental University stands.

In 1871, after the Meiji Restoration, Neo-Confucianism fell from official favor and the academy was closed, although it is considered one of the direct precursors of the University of Tokyo, which was established five years later.

Besides lessons, the Shosei students lived on campus and spent a lot of time scholarly debating among themselves, naturally creating a strong alumni network spanning all over the country, which was key during the Meiji restoration.

"Reading examination"), held yearly to evaluate younger trainees and whether they could continue or not their studies, to the prestigious Gakumonginmi (学問吟味, litt.

This building survived through the Meiji period, was used to host the Yushima Seidō Exposition in 1872, and was designated a national historical site in 1922, but was burnt down in the Great Kantō earthquake of the following year.