In 1993, a group of Catholic businessmen, educators, and lay leaders, under the spiritual direction of the Legionaries of Christ and with support and encouragement from the Archdiocese of Atlanta, founded Pinecrest Academy as an independent, private elementary school in North Atlanta. This farsighted community of parents, teachers, and supporters recognized a need for a unique center of learning and spiritual growth.

In its very first year, Pinecrest set a standard of academic excellence and spirituality which struck a responsive chord in parents who learned of its mission and experienced firsthand the academic and spiritual growth of their children. With an initial enrollment of 29 students, the school began in rented facilities in a former Fulton County elementary school in Crabapple, Georgia.

In 1995, Pinecrest moved to the religious education classrooms at All Saints Catholic Church in Dunwoody, where by the beginning of its fourth year of existence, enrollment had increased to the facility's maximum capacity of 153 elementary school students in pre-kindergarten through eighth grade. In March of 1998, Pinecrest received accreditation status from The Georgia Accrediting Commission, Inc.

In August of 1998, Pinecrest moved to its permanent home on 53 acres in South Forsyth County. The school began its sixth year of growth with a six building, 15-classroom facility and accreditation from the Southern Association of Colleges and Schools (SACS) in the young school's first year of eligibility.

In the fall of 2001, the Donoghue Building was completed and the campus expanded to 68-acres due to the generosity of a benefactor who donated an additional 15 adjoining acres. In 2003, the Gannon Building was completed making it possible for the Middle and High Schools to move into separate facilities. In 2007, the school graduated its first senior class.

In the fall of 2007, the community dedicated a beautiful 350-seat Chapel as well as an outdoor amphitheater-gifts from an anonymous benefactor. After its first full year, the High School was named one of the top 50 Catholic High Schools in the nation by the National Catholic Honor Roll.

Today, the facilities include a Lower School campus for Pre-Kindergarten through 5th grades, a classroom building for 6th through 12th grade boys, a classroom building for 6th through 12th grade girls, a gymnasium with cafeteria, a lighted football field, a baseball field, soccer field, cross country course, and two playgrounds. When fully completed, the campus will feature separate buildings for Lower, Middle, and High Schools, additional athletic fields, a commons building, a high school gymnasium, and fine arts and media centers. The buildings will each house computer and science labs, as well as chapels to enhance studies and spiritual growth.