Jews settled in Pergola in the early 13th century. The city was part of the Duchy of Montefeltro and offered Jews a tolerant environment. The two rivers favored trade, as well as the activities of the dyers and tanners.
The synagogue was originally located in a building that still stands in Via Don Minzoni, 9. The old Jewish cemetery has been identified on the road that led to the district of Mezzanotte, on land owned by the Medici family. An archaeological excavation began in 2005.