Favaios originally was part of the region of Panoias, before being occupied by Roman legions between 218 AD and 201 AD. Lost to the tribes of Lusitanians and Hispanic clans after 200 AD. The founders came from the families and relations of the Flavian dynasty, of Imperial Rome, who rose to prominence after Emperor Titus Flavius Caesar Vespasianus Augustus. The parishs' name is derived from Flávios, a corruption of the original Flavius of this leader. Panoias was a vast territory which extended from Marão to Tua Rivers, and from the Douro River until the municipality of Murça.
The invasion of the Iberian peninsula by Arabs reached the north, where the Moors took the Roman Castle of Flávias: it would later be remembered as the "Castelo dos Mouros”. This occupation forced the locals to escape the region and re-established settlements away from Favaios: half the population took refuge in the area that would be renamed São Bento. From this new colony the Portuguese battled the Moors of Favaios; after the expulsion of the Moors the region was covered in the destruction of these battles. The destruction lead to a slow reconstruction of Favaios.
Favaios received in 1211 its Carta de Alforria from King Afonso II, and its foral in 1270 by Afonso III. Strangely, during the reign of Manuel I the charter was revoked in 1514, to be reinstituted the following year, ordering that the local fountain be marked with the Royal shield over an armillary sphere, surmounted by a crown.
With an area of 21.45 km², Favaios is located along a plateau in the Trás-os-Montes e Alto Douro province, district headed by Vila Real de Trás-os-Montes city.