Conestoga Christian School was begun in 1952 by a group of parents from Conestoga Mennonite Church. That first year approximately twenty-two students studied in a rented school building.
On August 26, 1953, the Conestoga Christian Day School Association was chartered as a non-profit organization in Pennsylvania. A new building was constructed containing two rooms. The school had two teachers for grades one through nine. As the enrollment increased, more rooms were added to the first building, and in 1963 an elementary classroom building was erected.
In 1974 another building program was completed, adding four additional classrooms to the elementary building. A gymnasium/auditorium area, including classrooms, kitchen, stage, locker rooms, and library, was completed in 1988.
In 2005 the school completed a new high school wing including high school classrooms, a middle school science room, an enlarged media center, a new computer lab, and centralized office areas.