The school was established in 1970 as a segregation academy.

[2] Magnolia Heights School was founded by Nat G. Troutt, encouraged by a group of citizens who desired segregated education in the Tate County after desegregation.

In the school's first session in 1970–71, 233 students attended with the first senior class graduating fifteen students on the front campus of the school.

[1] The school was part of a wave of segregation academies that opened after the court ordered desegregation of Mississippi public schools.

[2] In 2017, the school claimed a 100% graduation rate, with 100% offered scholarships.