The Bay School campus is located in Building 35 on Keyes Avenue in the Main Post area of the Presidio. The campus is surrounded by expansive open space, providing spectacular views of San Francisco Bay and the Golden Gate Bridge, and is situated in the midst of the vibrant Presidio community--comprised of businesses, nonprofits and foundations focused on the environment, arts and culture, science, technology and global issues.

Built in 1912 for original use as army barracks, Building 35 is a spacious 62,000-square-foot building that has been designated as a national historic landmark. It underwent a complete year-long restoration in 2004-2005 designed to transform it into a state-of-the-art facility, the ideal home for a 21st-century high school. The Bay School campus has received numerous architectural and environmental awards.

The building is ideal for school use because of its high ceilings, large spaces, efficient traffic flow, and excellent natural light and ventilation. Bay School community spaces, such as the 3,000-square-foot Fulbright Library and the 4,500-square-foot student commons, called the Great Room, are located on the ground floor. A full-size catering kitchen provides delicious organic meals that are cooked on-site and shared by all members of the school community in the spacious 2,000-square-foot dining room. In an inviting outdoor courtyard adjacent to the dining, students enjoy eating together, socializing, and playing informal games of basketball and ping-pong on sunny days.

23 classrooms are located on the second and third floors of the building, intentionally interspersed with faculty offices to encourage close relationships between students and teachers. Three state-of-the-art science laboratory classrooms are located at the north and south ends of the upper two floors for physics, chemistry, and biology. On the third floor, the Digital Media Lab is situated directly across from the art studio to facilitate interaction between the two programs. The school's music, drama and dance programs are located on the basement level, which includes large classroom spaces for drama classes and rehearsals, choral and orchestral instruction as well as instrumental practice rooms.