The University High School, as the school was commonly known through the 80s, was founded in 1957 on a site overlooking the San Diego Bay to the west and Mission Valley to the south, and dedicated to providing value-centered education to San Diego's young men. In 1970, it merged with sister school Cathedral Girls' High School and became a co-educational campus. The decided name for the combined schools was (and still is) The University of San Diego High School. It maintained its emphasis on teaching solid values and strong discipline, while at the same time, providing opportunities for each student to grow according to his/her individual potential. Over 10,000 students have graduated from the school.

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The Linda Vista campus has held up to 1,450 students who study a college preparatory curriculum in fulfillment of the school mission to assist parents in the spiritual, intellectual and physical development of their children. Students were also offered opportunities to participate in a wide variety of extracurricular activities including fine arts, athletics, clubs, service organizations and leadership roles. Beginning with the 1998-99 school year, students were required to complete service hours for community organizations to fulfill their graduation requirements.

Alumni of USDHS and CGHS supported the educational process by sending their children to USDHS and enhancing the academic offerings. Brother Michael Wallgren, 1985-1991, assisted by a generous gift from the George Pflaum, Jr. Foundation, started the Learning Center at USDHS to provide necessary assistance for students with certified learning differences. Through the generous financial assistance of parents, this facility has increased its capacity to 90 students with two full-time and two part-time faculty.

Dr. Richard Kelly, Principal and President from 1991-2004, acted on the Strategic Plan prepared for USDHS with the assistance of the School Board, Parents Association, and Faculty. The Strategic Plan provides for academic, athletic, and social enhancement, often made possible only by physical plant improvements. Academically, there has been an expansion of the Fine Arts Program, the addition of eight new classrooms, and an increase of five Advanced Placement courses. The initial purchase of ten high-end research computers linked to the Internet and a new writing lab complemented the enhancement of the Campus Center building. The computer lab received all new iMac computers and all classrooms had a new computer and printer installed to allow teachers to write lessons, input grades, post homework and keep parents updated on student progress in 2000.

In 1999, The Diocese of San Diego announced plans for relocating USDHS to a new site, offering the needed space to expand their educational efforts. The final few years of the USDHS Presidio (The school's yearbook) were dedicated especially to UNI's final farewell. Cathedral Catholic has since picked up the Presidio tradition, and recently published the 50th copy.

On June 4, 2005, the 48th and final class to have attended all four years at the Linda Vista campus graduated. On June 9, 2005, the remaining underclassmen attended their final day at the USDHS campus. With the students gone for summer vacation, the teachers and faculty used the three months to make the transition to the new Carmel Valley location. Summer school successfully opened two weeks later at Cathedral Catholic High School. However, due to unfinished parts of the new campus, sports camps were held between both USDHS and CCHS.

On August 29, 2005, Cathedral Catholic High School opened its doors to the remaining three classes from University of San Diego High, as well as a new freshmen class who, in 2009, will be the first class to have attended CCHS for all four years.

The move to Cathedral Catholic High School has been a difficulty for students, teachers, and alumni to fully accept. Many still refer Cathedral Catholic as USDHS or Uni. Cathedral Catholic has attempted to continue all of the traditions founded at USDHS, from the mascot Dons to the academic, athletic and social awareness standards. Cathedral Catholic looks ahead, as always, to expand its educational efforts and continue its rigorous curriculum and legacy as the University Dons. Even though some people fear that the move to Cathedral Catholic has weakened the Dons spirit overall, many students stand behind each team, group, and aspect as they strive to do their best in all that is offered to them at CCHS.