The school was established in 1952 under the direction of the Parish Pastor, Reverend John G. Flack, and the Benedictine Sisters. The Sisters staffed the school until June 1972. Declining vocations required reorganization as they could no longer adequately staff the school. Through Reverend Flack's efforts, the Sisters of the Love of God, an order of Sisters from Spain, replaced the Benedictine Sisters in September 1972. This resulted in a smooth transition for the administration of the school.
In September 1952, the St. John's Classroom Building accommodated a student body of two hundred eighty students in grades one through five. Increased enrollment necessitated the construction of a second classroom building, the St. Elizabeth's Classroom Building. In the fall of 1994, the computer lab was moved to its present location from what is now Room 3A. During the summer of 1998, the smaller parish apartment building was renovated from a small school library to the Nugent Room, a multi-purpose room, serving as the St. John the Baptist Extended Care Center. In August 1998, the Kindergarten classroom building and the Faculty Lounge were dedicated. These buildings provide adequate classroom space and comfort-controlled environment for optimum learning setting for our students.