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.
The school opened in September 1971 with 118 students in kindergarten through sixth grade. The school added a seventh grade in 1972, an eighth grade in 1973, and a ninth grade in 1975. The school phased out the seventh, eighth, and ninth grades by 1981 to focus its efforts on an elementary education. The fall of 1989 was the beginning of the junior kindergarten program. In 2017, the school added a junior fours program to focus on capturing each child's curiosity while equipping them with the skills required to succeed in a school setting.
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.
The Heads of School for St. Paul include David Paulk (1971-1980), Leonard Garriott (1980-1983), Paul Hood (1983-1986), Thomas Hamilton (1986-1989), Lynn Husband (1989-1993), Martha Harris (1993-2000), and Ken Cheeseman (2000-2016). Dr. Jason Powell was named St. Paul's Head of School in August 2016 and began his role on July 1, 2017.