The name of the town comes from the Arab Ay-ndun meaning "higher water spring". The town was founded, probably on a previous Arab settlement by the Normans who came to Sicily under the leadership of Roger of Altavilla to fight the Arabs. Aidone is mentioned in 1150 in the "libro di Re Ruggero", and was at the time populated by the Lombards, who had fought in the Norman army. In the following centuries Aidone passed through many different dominions: the Swabians, Aragonese, Castillans, and finally the Bourbons (1700-1860).

Morgantina has been the main site of American research on classical Sicily. In 1955, a major project was begun by Princeton University, under the supervision of Professors Erik Sjöqvist and Richard Stillwell. The excavations on the (at that time unidentified) town were intended to serve as training for graduate students in Princeton's Department of Art and Archaeology. Special mention should also be made of Sweden's King Gustav VI Adolf, who came to Morgantina on several occasions in the 1950's at the invitation of Sjöqvist, his former secretary, to work at the site.

In the mid-1960's, Princeton graduate student Hubert L. Allen was hired by the University of Illinois, which then began to co-sponsor the Morgantina project. Allen continued to lead the project until the 1970's. The excavations had produced vast amounts of artifacts and data, but as yet there was no final publication. In 1978, Malcolm Bell III, professor of classical art and archaeology at the University of Virginia, took over the project with the goal of publishing the Morgantina material. In 1990, Carla Antonaccio of Wesleyan University, herself a Princeton graduate, assumed responsibility for publishing the post-7th century BCE settlement on Cittadella. Since that time, both Virginia and Wesleyan, along with many other American and Italian institutions, have sent scholars and students to conduct research. The site's archives are currently housed at the Department of Art and Archaeology at Princeton University, though some materials also exist at the University of Illinois.