The church dates back to the second half of the XIII Century; it has been an important Francescan Church of the city, annexed to the convent bearing the same name, site both of the minor friars and the Studium Medievale. Documents of the XII Century indicate that it has been built above the ancient church of Santa Susanna, whose name is the one of the whole District. It was built following the prototype of the Basilica di San Francesco in Assisi, with a superior church superimposed to the inferior one (ex Santa Susanna).
Often the church, along the centuries, suffered from problems relaing to stability, due to landslides and seismic activity; for this reason it has been often renovated. The containment interventions, such as the adding of Renaissance side chapels and the XVIII Century interior facings, even if meant ot stop the degradation, have altered the original features, weighting more on the surface floor; because of that the unsafe vaults were therefore demolished.
Once it was known as the “Pantheon” of Perugia as it received the remains of the city famous men – as the Beato Egidio, comrade of San Francesco – and of many notables Families of Perugia, who hordered the building of funerary monuments with artworks of great artists (Bonfigli, Perugino, Pinturicchio, Raffaello, Alfani, ecc...).
The collapses of the church facilitated the Napoleonic despoliations; one third of the artworks taken from Umbria were from San Francesco al Prato. The following passage to the Demanio (State Property Office) with the Unità d’Italia (Italian reunification, 1861) and new thefts have finished the damage.
After years of abandonment, in 1926 the restauration works started and it was decided to get back to the original Gothic Structure. The Façade has been totally rebuilt by Pietro Angelini as in origin, following the testimony of the painting by Benedetto Bonfigli (the Gonfalone di San Bernardino, 1465).
For several years the church apse was kept in the “natural setting” in open air; some evnets of Umbria Jazz were held there. In 1982 the Architect from Perugia Bruno Signorini proposed his first project for a city Auditorium. The earthquake of 1997 caused further damages that prolongued the works, now almost ended. The modern Auditorium with more than 500 seats willnot only be used for music concerts, but also for dance and theatre shows and other cultural events.
For what concerns the Convent complex, including the Oratorio di san Bernardino, since the beginning of XX Century, is home to the Accademia di Belle Arti Pietro Vannucci and its museum.