Boggs Academy was founded by the Reverend Dr. John Lawrence Phelps (1866–1937). The vision of Boggs Academy began during the summer of 1906, which was a year of extreme racial tension in the south. Amid this climate, Phelps accepted the challenge to establish a school built on Christian principles, which would educate African American youth. He set about building a church and school with the support of the Presbyterian church and the local community.

The initial two acres of land were donated by Morgan Walker, donations were collected, and a church was erected (Morgan Groove Presbyterian Church). By December of that year, the church doors were opened, and by January 1907, an independent school was opened in the church. Five children were enrolled in Boggs Academy when it opened. The school was named after Virginia P. Boggs (Corresponding Secretary of the Presbyterian Board of Missions For Freedmen) as a tribute for her faithful zeal, commitment to the school’s success and her support and friendship to Reverend Phelps while he was a student at Biddle University (now known as Johnson C. Smith University).