The origins of the Sant’Anna School date back to the late eighteenth century, when in 1785 the Grand Duke Peter Leopold of Lorraine founded the "St. Anne Conservatory" in Pisa in order to attend to "the education of young women of civil condition." The school is named after its first historical site, the former convent of St. Anne, a fourteenth-century Benedictine monastery, suppressed in 1786 as part of the Leopoldina reforms
The "Mussolini College for Corporate Sciences" had been founded in Pisa in 1931 and the "National Medical College" in 1932; they were attached to the Graduate School and later reorganized into the "Medical-Legal College." The "Antonio Pacinotti College" was created in 1951, including the faculties of Economics, Engineering and Agriculture. With Law no. 117 of 7 March 1967, the various colleges established a single "School of graduate and advanced studies," organized in the subject areas of "Social Sciences" and "Experimental and Applied Sciences," which settled in its current location between 1975 and 1979. In 1987, the Sisters of the conservatory, which was near to being closed, declared they were willing to sell it to the "School of graduate and advanced studies," provided that the whole complex would remain named after St. Anne; based on the model of the nearby Normal School, the "Sant’Anna School of graduate and advanced studies" was therefore established as a university institution with legal personality and administrative/disciplinary autonomy. At the same time, a library was created, which contains more than 70,000 volumes.