St. Patrick Catholic School was founded in September 1962, as a result, of the efforts of Father William O’Dwyer and a group of enthusiastic parishioners. The school opened with 181 students in grades one through seven and was staffed by four Sisters of Charity of the Blessed Virgin Mary. Due to grade combinations only four classrooms were used the first year. An additional classroom was used each year and all eight classrooms were utilized after 1969.

The Sisters of Charity left in 1976, due to a shortage of available personnel and the school was staffed by complete lay staff and principal for one year. In 1977 the Sisters of St. Clare came to the school, including four teachers and a principal. By 1988, only one Sister of St. Clare remained at the school and an Adrian Dominican sister became principal, however since 1996 the school has been staffed completely by lay personnel.

In 1988, a full day kindergarten was started and Spanish, music and a computer literacy program were added to the curriculum and additional teachers were hired for these classes. In 1989-90, the junior high wing was built, providing an extra classroom for computer classes. By 1990, St. Patrick Catholic School had an enrollment of 293 students in grades K-8, utilizing nine classrooms. An extended day care program, conducted in the first grade classroom, was established in 1992.

In the spring of 1994, an expansion committee was formed to explore the feasibility of expanding the school. In early 1995, the parish council and the Diocese of San Diego approved the expansion of St. Patrick Catholic School. A second kindergarten was added and the school added an additional class each year until all grades were doubled.

St. Patrick Catholic Community began a Capital Campaign, “Building Our Future…Together In Faith” in 2010 to finance enhancements for the Church, and construction of a new education center used for school and Parish activities and ministries. The newly renovated Church was completed and dedicated in February 2014. The second phase of the campaign, the school renovations, began in the summer of 2014 and was completed in November 2016.