For several years after the founding of the parish of the Holy Spirit in 1926, there was a great need for school facilities in the community. Through the efforts of the pastor, Father P. J. Concannon, and his congregation a Holy Spirit School was built.

In 1936, Holy Spirit School was opened and staffed by the Sisters of the Immaculate Heart of Mary. The charism of their order was education. Holy Spirit School opened with an enrollment of 275 children; serving the community of the parish of the Holy Spirit and the neighboring community of the parish of St. Agatha.  The original building still stands. It is of Italian architecture and was designed to accommodate 375 children.

In 1968, a shortage of vocations made it impossible for the Sisters of the Immaculate Heart of Mary to continue ministering the school, and the order withdrew. The Sisters of the Holy Faith, whose charism was also education, continued the great work at Holy Spirit School. The Sisters of the Holy Faith remained involved with the school until their departure from the convent at St. Mary Magdalen Parish in December of 2018.

Between 1970 and 1972, a consolidation of Holy Spirit School and St. Mary Magdalen School took place. They remained separate campuses serving four grade levels at each school.

In September of 1988, a full-day Kindergarten program was established at the Holy Spirit School campus site in order to meet the needs of the community.

In 2013, a Transitional Kindergarten program was established at Holy Spirit School to serve a younger population of children.

In January of 2019 the schools returned to a single campus at Holy Spirit School. The adoption of a STEM curriculum prompted the merger.