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Saint Charles Borromeo Parish was established in 1946 by Bishop Charles Buddy to serve the residents of Loma Portal and the large government housing project of the Midway area. The church complex was built directly across from the main gate of the Naval Training Center. The founding pastor, Monsignor Joseph N. Trivisonno, and the original parishioners set out to build a church, a school and convent. All of this was accomplished in a short space of time, and the newly created Saint Charles Borromeo Parish became a vibrant Catholic community. In 1947, just one year after the parish was founded, the academy was established. The academy opened on September 18, 1947, with grades kindergarten through eight.

An order of religious women from Staten Island, New York, the Daughters of Divine Charity, provided twelve sisters to staff the school. They were the only order which had given a favorable reply to 120 requests for educators to orders of women religious throughout the country. The Daughters of Divine Charity continued to work at the academy and provided a principal for the school until 1986. Since 1986, the school has had a lay person as administrator and has had a faculty of lay and religious members.

Our enrollment remains viable with 244 students in grades kindergarten through eight. Some of our students are the children or grand-children of alumni of Saint Charles Borromeo Academy. The summer of 1995 brought many structural changes to our school as the Sound Attenuation Project was implemented through the San Diego Port District. Renovations were done to lessen the impact of the noise from Lindbergh Field Airport.

We celebrated the 50th Anniversary of the parish and academy in October, 1996. The occasion brought back many former faculty members and alumni. The event was a testimony to the positive Christian witness of the parish and academy.

In 2001 the PTG modernized the computer lab and began plans for a preschool. In 2003 the academy adopted the Core Knowledge curriculum and full implementation of the Boy's Town Social Skills curriculum. Currently, our pastor Fr. Ed McNulty, the administration, parish and academy leaders, an architect and a contractor are collaborating to develop a plan to renovate the grounds, expand facilities and begin a capital campaign to build a preschool and library.

History of the Academy