Freeman Academy was chartered on December 14, 1900. Instruction began in the fall of 1903. Freeman Academy was part of the Freeman Junior College campus until the college closed in May, 1986. Grades 7 and 8 were then added in the fall of 1986 to the existing grades 9-12 program. In 1992, grades five and six were added to complete the Middle School program, and most recently, grades one through four were added in the fall of 2012. Freeman Academy and its programs are fully accredited by the State of South Dakota. Since 1968, Freeman Academy has been recognized as a related body of the Central Plains Mennonite Conference, Mennonite Church USA, formerly the Northern District Conference of the General Conference Mennonite Church. In 1987, Freeman Academy was accepted as a member of the Mennonite Secondary Education Council and now participates in its regular administrator meetings, biennial teacher convention and board workshop, and annual music festival. Freeman Academy operates under a private corporation consisting largely of various members of Mennonite churches. However, since its inception, the corporation and school participation has always included other denominations. There are no barriers of race, nationality, or creed.
Despite being a small school, Freeman Academy students rank high in all areas of learning and extra curricular activities.