It was founded by papal bull in 1538 in Santo Domingo, in the Caribbean island of Hispaniola, present-day Dominican Republic, although it didn't have the official certification by the king of Spain until 1558.

Founded during the reign of Charles I of Spain, it was originally a seminary operated by Catholic monks of the Dominican Order.

Later, the institution received a university charter by Pope Paul III's papal bull In Apostulatus Culmine, dated October 28, 1538.

Prior to its conversion into a full university, the institution had been a Studium Generale (seminary), founded in 1518 and operated by the Dominican Order.

And on November 16, 1914, President Ramón Báez, decreed its transformation into the Universidad Autónoma de Santo Domingo, successor of the first one.