The Bay School opened in the Presidio in 2004; at that time, a single class of 9th graders made up the student body.

[5] In August 2005, the school moved to 35 Keyes Avenue and has since added two nearby buildings in the Presidio.

[6][7] The school distributes $4.7 million in flexible tuition grants each year.

[8] Interdisciplinary and specialized courses include a study of water and politics in the American West, field geology, and biotechnology.

[9] The Bay School fields teams in 12 sports: Soccer, lacrosse, flag football, baseball, softball, basketball, volleyball, tennis, cross country, track and field, sailing, and golf.