The Institute was founded in 1784 by Grand Duke Peter Leopold of Lorraine, in accordance with the Archbishop of Pisa, Mons. Angelo Franceschi. In the 19th century the Institute became increasingly important, and in 1808 it was endowed with a meteorological observatory, to which was then added a seismic section, active until 1973. In the early 20th century, its educational activity was intensified. In the post-World War II years, the intermediate school became a State-recognised school, a recognition granted some years later to the secondary school as well, at the time a classic, now a scientific school.

The Institute possesses a collection of educational instruments belonging to the Physics Laboratory dating from the first half of the 19th century. The collection also includes human and animal models and anatomical specimens, as well as mineralogical and malacological collections.