The FIS Chaplaincy has had a long-standing relationship with Flandreau Indian School, its administration, staff and students. At the request of the students, Tony Firman served as Chaplain beginning in 1967. Since then opportunities to explore and deepen Christian faith have been consistently offered through the Flandreau Indian School Chaplaincy Program and its dedicated Chaplains.
In the early 1970s the Association of Christian Churches of South Dakota was the overseeing entity, with representation from the following denominations: Lutheran, Methodist, Presbyterian, American Baptist, Catholic, Disciples of Christ, Episcopal, Mennonite, Reformed, and United Church of Christ.
In 1997 the FIS Chaplaincy became a non-profit organization under the direction of an inter-denominational Board of Directors. Today, the corporation continues the legacy of providing for the physical and spiritual needs of the students and staff of Flandreau Indian School.