In the late 1950s and early 1960s the idea for a Catholic school was proposed by the families of St. Thomas the Apostle Parish. Families were interested in providing a quality education for their students in the Catholic tradition.

In the fall of 1964 ground was broken for the school at its current site on East Penn Street. Fr. Edward McConnell was the pastor of St. Thomas the Apostle at that time and is considered its' founder. The school was designed in a colonial style in keeping with the surrounding architecture of historic Bedford.

St. Thomas School opened on Wednesday, September 7, 1966 with four grades being instructed by nuns. Over the years St. Thomas School has expanded to include pre-Kindergarten classes through grade 6. The teaching staff now entirely consists of lay people, both Catholic and non-Catholic.

Although the demographics of the students and teachers have changed over the years, the mission to provide quality Christ-centered instruction remains.