It is one of four Catholic high schools in Sacramento affiliated with the Roman Catholic Diocese of Sacramento, and draws students from over fifty private and public feeder schools in the California counties of Sacramento, Yolo, El Dorado and Placer.

During the 2003–2004 school year, St. Francis completed the first phase of its campus renovation and expansion that doubled the size of its facilities.

These new buildings include The Fine and Performing Arts Complex, Library/Resource Center, Gymnasium/Fitness Complex, four science labs, the Administration Building, and the Carlsen and Demetre Center for Campus Life (CLC).

The school was run by the St. Francis Sisters of Penance and Christian Charity.

Bell appointed the Sisters of the Apostles of the Sacred Heart of Jesus, who served until 1999.