Founded in 1480 by Marsilius Ficinus in Florence, under the patronage of Lorenzo de Medici, the Academy is said by Freemasons of Tuscany to have been a secret society with a Masonic character. It is noted that the hall where its members held their meetings contained many Masonic symbols, according to Doctor Mackey's reports from his time.

Clavel (page 65, third edition, 1844) suggests that the Academy may have been established by some honorary members and patrons of the Fraternity of Freemasons who existed in the Middle Ages. According to this view, they abandoned the material design of the Institution and focused solely on its mystic character. If this suggestion is correct, the Academy represents one of the earliest instances of the separation of Speculative from Operative Masonry.