Its stated mission is "to transform human society through the most effective means possible, namely through training the youth in faith, reason, and virtue".

Primary grade teachers receive formal training in this method, which is child-centered and focuses on the physical and mental well-being of students.

Grades 6-8 emphasizes fundamental skill acquisition; accordingly, teachers employ a direct approach to instruction so that the student clearly understands the goal of each lesson at its beginning.

St. Joseph Academy's High School's college preparatory curriculum is approved by the University of California and meets its entrance requirements.

In addition to a wide offering of extracurricular clubs, its recognized athletic program includes membership in the North County Parochial League for middle school and the California Interscholastic Federation (C.I.F.).

In 1995, two Catholic mothers desired a school in North County (San Diego area) that would provide their children with both solid academics and faith formation within an integrated K-12 curriculum.

With all-volunteer labor and mostly donated materials, parents and other supporters cleared the lot, fenced in the area, installed irrigation, and planted grass.

In 2015, after receiving approval from city officials, the school embarked on a capital campaign to raise funds for Phase II of its campus, which will include science labs, additional classrooms, and a full-size gymnasium.

St. Joseph Academy's teachers come from a wide variety of professional backgrounds, including pontifical academia, law, the armed forces, government, and science.