In 1972, Saint Francis merged with Holy Cross High School, necessitating additional facilities.

In 2012, the school made a $15,000 investment into the tech company Snap Inc.; it had taken money from the endowment fund.

[6] In 2024, the school was sued by two students who were expelled after taking photos of themselves wearing face masks, perceived to be blackface.

The jury returned a split verdict on charges, but the school was ordered to pay $500,000 to each of the two students and to reimburse $70,000 in tuition fees.

Most of the student-athletes play in the West Catholic Athletic League part of the CIF Central Coast Section a subset of the California Interscholastic Federation.