In ancient times it was called Novempagi and Balneum Regium, whence the medieval name of Bagnorea.
During the barbarian invasions of Italy, between the sixth and ninth centuries, the city was taken several times by the Ostrogoths and the Lombards. Charlemagne is said to have included it in the Patrimonium Petri, and the Emperor Louis I to have added it to the Papal States in 822.
It is famous as the birthplace (more specifically Civita di Bagnoregio) of the philosopher St. Bonaventure in the early 13th century. Writer Bonaventura Tecchi also hailed from Bagnoregio.