St. Peter's was founded by priests belonging to the Society of Jesus (the Jesuits), a Roman Catholic men's religious order. It was established at Bird Tail Rock in 1871 after several previous locations were abandoned. Ursuline nuns joined the mission in October 1884 to assist in running the mission and teaching Native American children.

In 1884, the mission consisted of two log buildings -- a chapel with a bell tower connected to a common sleeping area for priests, and a lower structure which consisted of a sleeping area for nuns and a kitchen.

In 1887, private donations and a contract from the U.S. federal government to educate Native American chidren allowed the Jesuits to construct a three-story wood frame priests' residence. Attached to the residence was a four-story stone building with a mansard roof, dormers, and square cupola. The building contained dormitory space for male students, classrooms, a smithy, a cobbler shop, a carpentry shop, and a dining room. A kitchen garden was next to the building.

The Jesuits abandoned St. Peter's Mission in 1898, moving their educational and missionary activities to St. Mary's Mission on the Piegan Blackfeet reservation to the north. The boys' school burned to the ground in 1907. St. Peter's Mission was abandoned when the Ursuline convent burned to the ground in 1918.