Founded in 1700, the present building dates from 1785. It is open to the public except on Sundays when it is used as a church. The San Xavier Festival is held the evening of the Friday after Easter and features a torch-light parade of Tohono O'odham and Yaqui tribal members.
One of the more interesting historic features of the mission is that it is "unfinished". Early taxation rules dictated that missions under construction could not be taxed, so the mission was never finished, as noted by the absence of one dome.