Due to the Meiji Restoration, Shoheizaka Gakumonjo was condemned by the new government; Gakumonjo included Kaiseijo (which had a channel of tenmonkata (an astronomer appointed by bakufu)) and Igakusho (which had a channel of shutosho (vaccination institute)); they were reopened as a Shohei school, Kaisei school and medical school in 1869; these three became Daigaku Honko, Nanko and Higashiko in the same year and were later combined to be Daigakko, which was ultimately closed due to the revision of the school system in 1870.
明治維新では昌平坂学問所は新政府に接収され、併設された開成所（天文方の流れを組む）、医学所（種痘所の流れを組む）も共に1869年（明治2年）昌平学校、開成学校、医学校として再開し、同年大学本校、南校、東校となり、のち合わせて大学校となるが、1870年（明治3年）の学制改正で休校。