Founded in 1856, it is the second oldest continuously operating elementary school in California and serves families of the Diocese of San Jose.

In 1856 the Sisters of Notre Dame de Namur who came to create one of the earliest school systems in California founded St. Mary's School to educate elementary age students in the parish.

In 1924 Saint Clare moved across the street into a brand new school building that housed Kindergarten through eighth grade.

A Marble Plaque on the front of the school proclaims "DEO OPTIMO MAXIMO IN HONREM SANCTAE CLARAE XXI OCTOBRIS A.D. MCMXXIV DEDICATA" which translates to "To the greatest and best God in honor of St. Clare.

After more than 150 years of ministry, the Sisters transferred control of the school to lay leadership staff in 1998.