Like other artists in Rome he became involved in dealing in antiquities, and, with the financial backing of some British patrons, carried out several archeological digs.
In 1793 the visiting British Prince Augustus Frederick secured permission from the Pope for Fagan to export antiquities.
As an archaeologist he was involved in the excavations near Laurentum, which resulted in the discovery of the Venus, now at the Capitoline.
In 1809, following his daughter's marriage to William Baker, Fagan was made British Consul general in Sicily.
Fagan fell into debt, and committed suicide in Rome by jumping from a window.