The school is under the canonical jurisdiction of the Diocese of Stockton and sponsored by the Salesian order of the Oblates of St. Francis de Sales priests and brothers (Toledo–Ohio Province).

St. Mary's roots go back to 1876 when St. Agnes Academy opened as a boarding and free day school for girls, grades 1–12.

A separate corporation sole within the Diocese of Stockton, St. Mary's is a co-ed secondary school that has a student body of 926 and a faculty and support staff totaling over 110.

[citation needed] There are ten departments at St. Mary's from which students choose their required and elective courses: Theology, English, Social Studies, Mathematics, Physical Education & Health, Science, Computer, Foreign Language, and Fine Arts.

Honors courses are offered in Algebra, Biology, Chemistry, English, Geometry/Trigonometry, Physical Science, Pre-Calculus and World Literature.

As part of the religious focus of the school, each student is required to participate in a Community Service program upon graduation.