[4] SMCHS opened in the fall of 1987, the first Catholic high school to serve South Orange County.

SMCHS also offers a comprehensive Auxiliary Studies Program (ASP) to help students who learn differently than others.

[20] The spiritual aspect of Santa Margarita is developed within students through religious education classes, school wide masses, and various retreats throughout the year.

Included within credits completed satisfactorily are the following course requirements:[22] Students are expected to meet all Christian Service obligations before graduation.

[24] These activities include ASB/Student Council, Color Guard, Drama Productions, Mock Trial, and Pep Squad.

[25] Santa Margarita Catholic High School's athletic teams, known as the Eagles, compete in the Trinity League.

[27] has produced many distinguished athletes such as NBA All-Star Klay Thompson, Heisman Trophy winner Carson Palmer, Olympic gold medalist and winner of the 2015 FIFA Women's World Cup Amy Rodriguez, Outland Trophy recipient Kris Farris, Buffalo Sabres first-round draft pick Ryan Johnson, and recipient of the Walter Payton Award and Atlanta Falcons wide receiver Brian Finneran.

[13] SMCHS participates in 15 sports: football, volleyball, basketball, soccer, water polo, cross country, golf, tennis, wrestling, baseball, softball, lacrosse, ice hockey, track and field, and swimming.