The Faribault House was built in 1839 originally as a tavern when the young town of Mendota was then part of the Michigan Territory. This structure featured locally quarried stone with basement storage vaults for large quantities of food and liquor. The two upper floors were built with hand-hewn studs with willow branches interwoven between them, packed with mud, straw, and covered with plaster. The house also originally featured a ballroom and a frame structure with a kitchen and sleeping quarters at the rear.

The house was originally built for Jean Baptiste Faribault, a well-known fur trader and farmer for Fort Snelling who, in 1820, became the first settler of Mendota and Dakota County. The house and grounds were presented to and served as a chapel and residence for the Jesuit missionary, Father Galtier before the completion of the Church of Saint Peter in 1853, to which Galtier was never named as pastor – preferring to continue his missionary work instead. The house passed through other ownership over the years serving for some time as a hotel and later as a storage warehouse. The Faribault House was restored first in 1936 by the Minnesota Highway Commission (now the Minnesota Department of Transportation) as part of a Civil Works Administration project. The house (and other historic Minnesota houses) were then donated to the Daughters of the American Revolution (DAR). The DAR turned over management of the house to the Minnesota Historical Society which restored the house again in the 1980s.