- A.P. Giannini Middle School
- Alice Fong Yu Alternative School
- Alta Vista School
- Aptos Middle School
- Bessie Carmichael School
- Buena Vista Horace Mann
- Cathedral School for Boys
- Children's Day School
- Creative Arts Charter School
- Crystal Springs Uplands School
- Everett Middle School
- Francisco Middle School
- Gateway Middle School
- Herbert Hoover Middle School
- James Denman Middle School
- James Lick Middle School
- Katherine Delmar Burke School
- KIPP San Francisco Bay Academy
- La Scuola International School
- Live Oak School
- Marin Country Day School
- Marina Middle School
- Martin Luther King Jr. Academic Middle School
- Millennium School
- Mission Dolores Academy
- New School of San Francisco
- Paul Revere School
- Presidio Hill School
- Presidio Knolls School
- Presidio Middle School
- Rooftop School (Mayeda)
- Roosevelt Middle School
- San Francisco Friends School
- St. Anthony-Immaculate Conception School
- St. Peter's Catholic School
- Stella Maris Academy
- Sterne School
- Synergy School
- The Fr. Sauer Academy
- The Hamlin School
- The Mission Preparatory School
- The Nueva School
- The San Francisco School
- Thomas Edison Charter Academy
- Town School for Boys
- Visitacion Valley Middle School
- Westborough Middle School
- Willie L. Brown Jr. Middle School