The Presbyterian Church established a small mission school in 1872, part of a wave of schools that popped up on or in service of tribal lands and reservations. “In service of” is a relative term here; while children at these schools did often receive a good education, much of that education was intended to assimilate Native American children into Anglo-Saxon culture, teaching them English and Christianity.

When the school first opened, classes were taught in a church and meeting house, but a larger church was constructed the following year to accommodate the growing population of Native American families moving to the area. The following year, in 1873, children of local settlers began attending the school, and the federal government stepped in to provide funding for classroom supplies. The Bureau of Indian Education fully took over operation of the school in 1877.

Once South Dakota became a state in 1889, its newly elected Senator R. F. Pettigrew campaigned congress to appropriate funds for a new boarding school. The Flandreau Industrial Indian School, which included dormitories for boarding students, finished construction in 1892.

Though FIS has been in continuous operation since its founding, certainty about its future has ebbed and flowed. Several attempts have been made to close the school down, but the people in the area regularly rally to its defense. Today, FIS serves as a boarding school for Native American children, primarily members of the Lakota, with their tuition and board paid for by the Bureau of Indian Education. It is one of four off-reservation schools still operating under the auspices of the Bureau.