The Reverend John Scanlan built St. Thomas More School while he served as the first pastor (1950-54) of St. Thomas More Parish. In 1954, Monsignor Vincent Carroll succeeded Fr. Scanlan, who had just been named Bishop of Hawaii. Msgr. Carroll, who served as pastor from 1954 until 1985, oversaw the opening of the school in 1954 with grades one through four. A grade was added each year until the full complement of eight grades was reached in 1958. The first graduation was in June of 1959. A half day kindergarten program was added to the school in September 1980. That program became a full day program in September 1986.
The school was staffed by Sisters of Charity of the Blessed Virgin Mary (BVM) from its opening until 1980. At that time a Sister of the Notre Dame de Namur assumed the principalship for five years. At the start of the 1986-87 school year, Joe Elsbernd, a native San Franciscan and product of BVM education, was named principal by Fr. John Ring. Fr. Ring succeeded Msgr. Carroll and served as the third pastor of the parish until 1993. With Mr. Elsbernd, the BVM sisters returned filling roles in the parish and the school. Sr. Patricia Rogers, BVM served as vice-principal at the school from 1986 until her retirement in 2011.