In 1999, members of a home-schooling co-operative called Grace Cottage gathered to discuss the need for a Christian school focused on "parent based education".

Heritage Academy was soon formed to fulfill this need and, in fall 2002, the school began serving twelve families and 22 students.

The school was housed in Calvary Baptist Church on Ridgeway Avenue in Columbia until it moved to its current location in 2019.

Secondary teachers have greater freedom to design a syllabus as they prefer, though Heritage does abide by NAUMS standards.

To remain in good standing with an athletic team, participants must maintain a minimum of 70% in each class in which they are currently enrolled at Heritage, home or any other institution.

[14] Heritage Academy is co-located with Higher Ground Church at 2900 Barberry Avenue, Columbia, MO 65202,[15] although the school itself has no denominational affiliation.