St. Paul Christian Academy was founded in 1971 by St. Paul Southern Methodist Church (now St. Paul Community Church) and chartered as its own, independent, not-for-profit corporation.

St. Paul opened in September of 1971 with 118 students in kindergarten through sixth grade. A seventh grade was added in 1972, an eighth grade in 1973, and a ninth grade in 1975. Choosing to focus its efforts on kindergarten through sixth grade, the school phased out the seventh, eighth, and ninth grades by 1981. The fall of 1989 was the beginning of the junior kindergarten program. St. Paul was accredited by the Southern Association of Schools and Colleges (SACS) in 1996, reaccredited by SACS in 2002, and reaccredited by SACS and the Southern Association of Independent Schools (SAIS) in 2007 and 2012.  

In August of 2016, Dr. Jason Powell was named St. Paul's next Head of School. Ken Cheeseman assumed the role of Head of School in June of 2000 and will end his faithful service to the school in December. St. Paul’s previous Heads of School are David Paulk (1971-1980), Leonard Garriott (1980-1983), Paul Hood (1983-1986), Thomas Hamilton (1986-1989), Lynn Husband (1989-1993), and Martha Harris (1993-2000).