| The Discovery Center School | Redwood City | 3-10 | 6 | 4.3 | Nonsectarian |
| Adda Clevenger School | San Francisco | K-8 | 143 | 4.5 | Nonsectarian |
| Alta Vista School | San Francisco | K-8 | 323 | 6.3 | Nonsectarian |
| Archbishop Riordan High School | San Francisco | 9-12 | 1,143 | 14.9 | Roman Catholic |
| Arise Educational Center | San Francisco | 5-12 | 21 | 7 | Nonsectarian |
| Bais Menachem Yeshiva Day School | San Francisco | K-8 | 57 | 3.6 | Jewish |
| Brightworks | San Francisco | K-12 | 116 | 7.2 | Nonsectarian |
| Casa Dei Bambini School | San Francisco | PreK-1 | 40 | 10 | Nonsectarian |
| Cathedral School for Boys | San Francisco | K-8 | 256 | 6.2 | Episcopal, all-boys |
| Children's Day School | San Francisco | PreK-8 | 394 | 5.7 | Other religious |
| Chinese American International School | San Francisco | PreK-8 | 431 | 9 | Nonsectarian |
| Chinese American Intl Middle School | San Francisco | 6-8 | 122 | 8.7 | Nonsectarian |
| Cielito Lindo Montessori School | San Francisco | PreK-K | 2 | not reported | Nonsectarian |
| Convent & Stuart Hall Schools of the Sacred Heart | San Francisco | K-12 | 1,198 | 10.3 | Roman Catholic |
| Cornerstone Academy | San Francisco | K-8 | 363 | 18.1 | Baptist |
| Cornerstone Academy-Cambridge Campus | San Francisco | 4-8 | 184 | 16.7 | Christian (nondenominational) |
| Dahlia School, the | San Francisco | PreK-K | 1 | not reported | Nonsectarian |
| De Marillac Academy | San Francisco | 4-8 | 106 | 9.6 | Roman Catholic |
| Donum Dei Classical Academy | San Francisco | K-8 | 66 | 7.9 | Christian (nondenominational) |
| Ecole Notre Dame Des Victoires School | San Francisco | K-8 | 271 | 12.4 | Roman Catholic |
| Edgewood Center for Children & Families | San Francisco | 9-12 | 22 | 7.3 | Nonsectarian |
| Eureka Learning Center | San Francisco | K-Transitional K | 18 | 6.9 | Nonsectarian |
| French American Intnl School Preschool | San Francisco | PreK-3 | 322 | not reported | Nonsectarian |
| Fusion Academy San Francisco | San Francisco | 6-12 | 33 | 2.7 | Nonsectarian |
| Golden Bridges School | San Francisco | PreK-8 | 105 | 4.1 | Nonsectarian |
| Hillwood Academic Day School | San Francisco | K-8 | 26 | 6.8 | Nonsectarian |
| Holy Name Elementary School | San Francisco | PreK-8 | 364 | 19.6 | Roman Catholic |
| Ica Cristo Rey Academy | San Francisco | 9-12 | 270 | 14.2 | Roman Catholic, all-girls |
| Jewish Community High School of the Bay | San Francisco | 9-12 | 179 | 4.9 | Jewish |
| Kahlon Family Services School | San Francisco | K-4 | 10 | 3 | Nonsectarian |
| Katherine Delmar Burke School | San Francisco | K-8 | 401 | 8.3 | Nonsectarian, all-girls |
| Katherine Michiels School | San Francisco | PreK-5 | 17 | 3.2 | Nonsectarian |
| Kittredge School | San Francisco | K-8 | 60 | 4.6 | Nonsectarian |
| KZV Armenian School | San Francisco | PreK-8 | 98 | 7.5 | Other religious |
| La Scuola International School | San Francisco | PreK-8 | 233 | 7.7 | Nonsectarian |
| La Scuola International School-Mission Campus | San Francisco | PreK-8 | 233 | 7.7 | Nonsectarian |
| Live Oak School | San Francisco | K-8 | 415 | 6.1 | Nonsectarian |
| Millennium School of San Francisco | San Francisco | 6-8 | 104 | 7.8 | Nonsectarian |
| Mission Dolores Academy | San Francisco | K-8 | 173 | 10.6 | Roman Catholic |
| Mission Montessori | San Francisco | PreK-5 | 76 | 12.7 | Nonsectarian |
| Montessori House of Children | San Francisco | Transitional K | 30 | 3.8 | Nonsectarian |
| Nativity HS | San Francisco | 9 | 15 | 6.5 | Roman Catholic |
| Our Lady of the Visitacion School | San Francisco | K-8 | 216 | 19.6 | Roman Catholic |
| Presidio Hill School | San Francisco | K-8 | 210 | 6.5 | Nonsectarian |
| Presidio Knolls School | San Francisco | PreK-8 | 269 | 5.5 | Nonsectarian |
| Proof School | San Francisco | 6-12 | 113 | 5.5 | Nonsectarian |
| Red Bridge | San Francisco | K-5 | 40 | 5.5 | Nonsectarian |
| Rise University Preparatory | San Francisco | 9-12 | 72 | 8.2 | Christian (nondenominational) |
| San Francisco Adventist School | San Francisco | K-8 | 10 | 5 | Seventh-Day Adventist |
| San Francisco Christian School | San Francisco | PreK-12 | 264 | 15.6 | Baptist |
| San Francisco City Academy | San Francisco | K-8 | 86 | 4.9 | Christian (nondenominational) |
| San Francisco High School of the Arts | San Francisco | 5-12 | 48 | 2.5 | Nonsectarian |
| San Francisco Islamic School | San Francisco | K-8 | 72 | 9.5 | Islamic |
| San Francisco Pacific Academy | San Francisco | K-8 | 56 | 4.6 | Nonsectarian |
| San Francisco School | San Francisco | PreK-8 | 236 | 8.4 | Nonsectarian |
| San Francisco Schoolhouse | San Francisco | K-8 | 115 | 7.6 | Nonsectarian |
| San Francisco University High School | San Francisco | 9-12 | 480 | 8.1 | Nonsectarian |
| San Francisco Waldorf School | San Francisco | PreK-12 | 334 | 3.7 | Nonsectarian |
| School of the Epiphany | San Francisco | K-8 | 158 | 19.8 | Roman Catholic |
| St. Anne Elementary School | San Francisco | K-8 | 241 | 16.6 | Roman Catholic |
| St. Anthony - Immaculate Conception School | San Francisco | K-8 | 164 | 18.2 | Roman Catholic |
| St. Brendan School | San Francisco | K-8 | 277 | 19 | Roman Catholic |
| St. Brigid School | San Francisco | PreK-8 | 71 | 6.7 | Roman Catholic |
| St. Cecilia School | San Francisco | K-8 | 503 | 20.1 | Roman Catholic |
| St. Finn Barr Catholic School | San Francisco | K-8 | 224 | 18.7 | Roman Catholic |
| St. Gabriel Elementary School | San Francisco | PreK-8 | 511 | 17.7 | Roman Catholic |
| St. Ignatius College Preparatory | San Francisco | 6-12 | 1,585 | 12.4 | Roman Catholic |
| St. James Catholic School | San Francisco | K-8 | 111 | 15.9 | Roman Catholic |
| St. John of San Francisco Orthodox Academy | San Francisco | K-12 | 37 | 3.7 | Other religious |
| St. John the Evangelist School | San Francisco | K-8 | 152 | 11.8 | Roman Catholic |
| St. Pauls | San Francisco | K-8 | 165 | 14 | Roman Catholic |
| St. Peter's School | San Francisco | K-8 | 178 | 17.1 | Roman Catholic |
| St. Philip School | San Francisco | K-8 | 207 | 18.6 | Roman Catholic |
| St. Stephen School | San Francisco | PreK-8 | 240 | 18.5 | Roman Catholic |
| St. Vincent de Paul School | San Francisco | K-8 | 202 | 16.7 | Roman Catholic |
| Sterne School | San Francisco | 4-12 | 181 | 6.6 | Nonsectarian |
| Stratford School | San Francisco | PreK-4 | 69 | 6 | Nonsectarian |
| Stratford School San Francisco | San Francisco | 6-8 | 115 | 7.8 | Nonsectarian |
| Sts Peter & Paul School | San Francisco | K-8 | 168 | 13.1 | Roman Catholic |
| Synergy School | San Francisco | PreK-8 | 189 | 9.2 | Nonsectarian |
| The Bay School of San Francisco | San Francisco | 9-12 | 447 | 7.3 | Nonsectarian |
| The Brandeis School of San Francisco | San Francisco | K-8 | 360 | 6 | Jewish |
| Town School for Boys | San Francisco | K-8 | 416 | 5.8 | Nonsectarian, all-boys |
| Wen Jian Ying | San Francisco | 10-12 | 6 | 3.8 | Christian (nondenominational) |
| West Portal Lutheran School | San Francisco | K-8 | 330 | 14 | Lutheran Church (Missouri Synod) |
| Zion Lutheran School | San Francisco | K-8 | 152 | 11.9 | Lutheran Church (Missouri Synod) |