In 1966, a spirited group of preschool teachers and preschool parents conceived of a new school. They sought a community where parents and teachers could share in school governance, and where preschool children could thrive in a program guided by the principles of Maria Montessori, the Italian physician and educator who believed in every child's ability to learn. Five parents and four teachers signed the original Articles of Incorporation in March of 1966. The San Francisco Montessori School opened the following September. Tucked away in a church basement in the quiet Portola District, a working class San Francisco neighborhood, The School had just seven preschool students on opening day. The financial capital to stock the school with equipment and supplies came from a $100 per student "enrollment fee." The song, "'Tis a Gift to be Simple, 'Tis a Gift to be Free," that SFS students still sing today, certainly fit the school culture and finances of the time.

The successful new school grew quickly in popularity and population. In 1969, The School purchased the present property at 300 Gaven Street. Inspired by parent interest as much as preconceived design, the School added a first grade, and then grew organically in the 1970's up through the fifth grade, and to an enrollment of 145 students. The elementary curriculum consciously developed away from the traditional Montessori method to a progressive approach, incorporating Montessori ideals of self-reliance, responsibility, and learning through experience, but also embracing the best of current teaching practices. In the 1980's The School added an innovative Middle School Program. The School changed its name to The San Francisco School, grew to an enrollment of 225, established an endowment, and became known for its enthusiastic and well-prepared graduates.

The 1990's were years of consolidation, fund raising and construction. The San Francisco School entered the new millennium with extensive renovations, a new building, a Middle School expanding to two classes per grade level, and a reworded mission statement that keeps The School true to its founding spirit: