The territory of Fregona was already inhabited in Pre-Roman Age. The findings of utensils testify to a human presence dating back to the Iron Age, as also do Paleovenetians discoveries and a "Castelliere" (fortified village usually surrounded by walls), North of Saint Daniel's church. This sunny area, protected by the mountains and rich in water, was a suitable place to live. During the Roman Era Fregona became an important crossroad. Traces of this are found in names given to local spots and on antique Roman coins discovered locally.
Fregona with its surroundings later fell under the authority of the Bishop of Belluno, then under the rule of the Da Camino noble family. Testimonies are the ruins of the Castle of Piai and a wooden coffer strengthened with iron sheets, a real jewel of the local craftsmanship, discovered in 1500 and now kept in the local church.
In 1422 Fregona became part of the territories of the Republic of Venice. In 1509, during the League of Cambrai war, a quick action by a group of people from Fregona was crucial in liberating Serravalle (now part of Vittorio Veneto) from the Hapsburgs and giving it back to the Serenissima (Republic of Venice). As a result Fregona was conferred with its official Coat of Arms and the "Gastaldia" (a specific area under the Venetian administration) was exempted from wine taxes. The related document is still extant in the Town Hall.
In 1798 some families from the Asiago plateau migrated to the Cansiglio area, establishing a remarkable Cimbrian community. When the present road from Fregona to Cansiglio was opened, their descendants travelled down to Fregona in order to sell their handcrafted products, mostly wooden tools and boxes. Hence their nickname "Scatoleri" (box makers).