The Brafferton was constructed in 1723, likely by Henry Cary, Jr.,[1] to house the College's Indian school, which was endowed by funds from an estate purchased by the charity of Robert Boyle, the noted English scientist.

Income from Brafferton Manor in Yorkshire, England, designated for charitable and pious purposes, was used to "civilize" Indian youth, prepare them for Anglican priesthood — and produce interpreters and cultural liaisons who could aid Britain's colonial expansion.

Virginia's efforts to encourage allied and neighboring tribes to send Indian youth to Williamsburg were more successful, and several Brafferton students were key players in the late eighteenth century wars of North America.

It received additional renovation in 2010–13, a period in which the College of William & Mary established the Brafferton Legacy Group in conjunction with alumni from the school's tribal descendant communities, the Department of Anthropology, the College's American Indian Resource Center, Colonial Williamsburg's (CW) Department of Archaeology, and CW's American Indian Initiative.

[citation needed] The College and CW hosted a ground blessing for the start of archaeological investigations at the Indian school, and several Pamunkey tribal members worked on the 2011-12 excavations.

The building was rededicated in 2013 with opening remarks in the Cherokee language and honor songs, alongside greetings from the President of William & Mary and College Provost.