St. Philip's Episcopal School was established by action of the church vestry in 1954, becoming the first Protestant parochial school in Bee County. The Rev. John Worrell, then the rector of St. Philip's Church, was the first Headmaster.

The school originally had one small section of kindergarten children who attended class in the parish hall. Since then, the school has grown substantially, in both its enrollment and physical plant.

During the summer of 1980, the present brick structure was constructed for additional classroom space, with expansions in 1983 and 1992, due to generous grants and gifts from the James R Dougherty, Jr. Foundation and Board of Directors of the State Bank and Trust.

During the spring of 1993, a challenge gift of $300,000 from the most generous of school friends, Mrs. Jody Hughes, began a campaign which raised funds for a new school wing, as well as an addition for the existing parish hall. Construction was complete in the spring of 1994 on the building, which houses first through sixth grades, and Spanish, Art/Computer and Science classes. In 2016, the school purchased a modular building, named the Tom and Judith Healey Educational Annex, for the music instruction classes.