The purpose of the Saint Anne School Student Council is to work for the greater good of the student body by providing an opportunity for student expression, developing leadership, improving school spirit, and promoting positive citizenship and school ambassadorship. A particular emphasis is placed on school-wide service learning projects and charitable giving. Student Council designs and plans monthly fundraising opportunities and selects charities to benefit from their efforts. As well as annually supporting two orphanages in Tijuana, they have benefitted Autism Speaks, Cancer Charities, the World Wildlife Foundation, and many more.
Student Council is open to students in Grades 4–8. Elections are held in the Spring, with speeches, campaigning, and voting. Student leaders meet weekly to plan and oversee matters of school governance and school-wide charitable efforts.