Westover Christian Academy was founded as Southall Christian School in 1977 with 25 students enrolled in kindergarten through fourth grade. The school was located at 502 Southampton Avenue in Danville, Virginia, and was sponsored by Southall Baptist Church. One grade was added each year, and SCS graduated its first senior class of six students in 1986. Preschool classes including K-4 and K-3 were added in 1992 and 1993, respectively. A K-2 Preschool class was added in 2014.

In October 1993, Southall Baptist Church and Lynn Haven Baptist Church (located on Highway 58, west of Danville) merged to become Westover Baptist Church, using the previous Lynn Haven facility. In September 1994, Southall Christian School became Westover Christian Academy and moved into new facilities built adjacent to Westover Baptist Church at 5665 Riverside Drive. An enrollment of approximately 450 students quickly filled the eighteen new classrooms, computer lab, two science labs, cafeteria, offices, gymnasium, and locker rooms. New school colors (red, black, and white) and school mascot (the bulldog) were adopted.

WCA became fully accredited in 1997 by the American Association of Christian Schools. In 1998, a 20,000 square foot addition was completed, providing a band room, enlarged cafeteria, new library, and 12 additional classrooms to accommodate nearly 700 students. A satellite campus in Eden, NC, operated from 1999-2003 offering preschool through third grade with an enrollment of nearly 50 children. In 2002 WCA became a member of the Association of Christian Schools International (ACSI). Accreditation was transferred from AACS to ACSI in December 2002 and WCA has been fully accredited by ACSI since that time. In 2012, WCA received its AdvancED (SACS) accreditation. Every five years WCA must be reaccredited, with the most recent reaccreditation being completed in May 2019 by ACSI.