| Rise Institute | 1.2 |
Special education | 4-12 | 44 | 14.7 | Nonsectarian |
| Cornerstone Academy | 1.7 |
Regular elementary or secondary | Pre-KG-12 | 1058 | 13.6 | Baptist |
| Joshua Marie Cameron Academy | 1.8 |
Special education | 6-12 | 12 | 6.0 | Nonsectarian |
| San Francisco Waldorf School | 2.9 |
Special program emphasis | KG-12 | 407 | 10.3 | Nonsectarian |
| Sterne School | 2.9 |
Special education | 6-12 | 50 | 4.4 | Nonsectarian |
| Hergl School | 3.3 |
Special education | Ungraded-Ungraded | 8 | 8.0 | Nonsectarian |
| Lycee Francais La Perouse - San Francisco Campus | 3.3 |
Special program emphasis | Pre-KG-12 | 864 | 24.0 | Nonsectarian |
| Sr Martin College Preparatory School | 3.3 |
Regular elementary or secondary | 6-12 | 29 | 7.6 | Other |
| Lisa Kampner Hebrew Academy | 3.4 |
Regular elementary or secondary | Pre-KG-12 | 132 | 6.7 | Jewish |
| San Francisco Christian School | 3.5 |
Regular elementary or secondary | Pre-KG-12 | 224 | 14.0 | Baptist |
| Erikson School | 4.0 |
Special education | 4-12 | 21 | 7.0 | Nonsectarian |
| St John Of San Francisco Orthodox Academy | 4.2 |
Regular elementary or secondary | KG-12 | 48 | 3.7 | Other |
| Roger Williams Academy | 6.7 |
Regular elementary or secondary | 1-12 | 25 | 8.1 | Baptist |
| Pentecostal Way Of Truth Academy | 7.4 |
Regular elementary or secondary | KG-12 | 15 | 1.6 | Nonsectarian |
| Asa Academy | 8.7 |
Regular elementary or secondary | 6-12 | 49 | 3.4 | Nonsectarian |
| St Andrew Missionary Baptist Church Pvt School | 8.9 |
Special program emphasis | KG-10 | 45 | 22.5 | Baptist |
| Children's Learning Center | 9.0 |
Special education | KG-12 | 72 | 7.1 | Nonsectarian |
| Children's Learning Center | 9.2 |
Special education | Ungraded-Ungraded | 23 | 5.8 | Nonsectarian |
| Highlands Christian Schools | 9.3 |
Regular elementary or secondary | Pre-KG-12 | 613 | 17.3 | Christian (no specific denomination) |
| Oak Hill School | 9.5 |
Special education | 1-12 | 20 | 5.0 | Nonsectarian |
| Agnes Memorial Christian Academy | 10.1 |
Regular elementary or secondary | Pre-KG-12 | 15 | 3.8 | Pentecostal |
| Via Center | 10.2 |
Special education | Ungraded-Ungraded | 18 | 9.0 | Nonsectarian |
| Beyt Hasepher | 10.6 |
Alternative/other | 1-12 | 19 | 2.4 | Christian (no specific denomination) |
| Patten Academy Of Christian Education | 11.0 |
Regular elementary or secondary | KG-12 | 197 | 12.2 | Christian (no specific denomination) |
| Clara Mohammed School | 11.4 |
Regular elementary or secondary | KG-12 | 27 | 5.1 | Islamic |
| Wings Learning Center | 11.4 |
Special education | Ungraded-Ungraded | 17 | 5.7 | Nonsectarian |
| The Renaissance School | 11.5 |
Montessori | Ungraded-Ungraded | 147 | 6.1 | Nonsectarian |
| Alma Heights Christian Academy | 12.2 |
Regular elementary or secondary | KG-12 | 295 | 12.0 | Other |
| Elim Christian School/colegio Evangelico Elim | 12.8 |
Regular elementary or secondary | KG-12 | 44 | 7.3 | Christian (no specific denomination) |
| Family Christian Academy | 13.0 |
Regular elementary or secondary | Pre-KG-12 | 7 | 3.9 | Pentecostal |
| Candell's College Preparatory Academy | 13.2 |
Regular elementary or secondary | KG-12 | 60 | 13.6 | Christian (no specific denomination) |
| Stanbridge Academy | 13.2 |
Special education | Ungraded-Ungraded | 93 | 4.9 | Nonsectarian |
| Arlington Christian School | 14.2 |
Regular elementary or secondary | KG-12 | 49 | 9.2 | Baptist |
| Crystal Springs Uplands School | 14.2 |
Regular elementary or secondary | 6-12 | 350 | 6.6 | Nonsectarian |
| King's Academy | 14.3 |
Regular elementary or secondary | 1-12 | 42 | 1.7 | Christian (no specific denomination) |
| Chinese Christian Schools | 15.7 |
Special program emphasis | KG-12 | 915 | 11.0 | Christian (no specific denomination) |
| Calvary Christian Academy | 16.0 |
Regular elementary or secondary | Pre-KG-12 | 150 | 12.5 | Christian (no specific denomination) |
| East Bay Waldorf School | 16.0 |
Special program emphasis | KG-12 | 269 | 7.3 | Nonsectarian |
| Community Christian School | 16.1 |
Regular elementary or secondary | KG-12 | 147 | 11.3 | Assembly of God |
| Bethel Christian Academy | 16.7 |
Regular elementary or secondary | KG-12 | 85 | 13.9 | Baptist |
| International Bible Baptist Academy | 16.8 |
Regular elementary or secondary | KG-12 | 39 | 4.4 | Baptist |
| A Better Chance School/cal Autism Foundation | 16.9 |
Special education | 1-12 | 37 | 6.2 | Nonsectarian |
| Seneca Center | 17.0 |
Special education | 1-12 | 113 | 9.7 | Nonsectarian |
| El Sobrante Christian School | 17.0 |
Regular elementary or secondary | KG-12 | 399 | 12.3 | Assembly of God |
| Alpha Beacon Christian School | 17.0 |
Regular elementary or secondary | Pre-KG-12 | 152 | 11.9 | Christian (no specific denomination) |
| Spectrum Center - Tara Hills | 17.6 |
Special education | Ungraded-Ungraded | 104 | 9.4 | Nonsectarian |
| Star Academy | 17.7 |
Special education | 3-11 | 69 | 11.9 | Nonsectarian |
| James R Sylla/sunny Hills Services | 17.8 |
Special education | Ungraded-Ungraded | 31 | 6.1 | Nonsectarian |
| Stinson Beach Montessori School | 19.0 |
Montessori | Ungraded-Ungraded | 1 | 1.0 | Nonsectarian |
| Mulberry Classroom | 19.7 |
Special education | KG-11 | 18 | 3.5 | Nonsectarian |
| West Bay High | 20.1 |
Regular elementary or secondary | Ungraded-Ungraded | 49 | 12.9 | Nonsectarian |
| San Domenico School | 20.2 |
Regular elementary or secondary | KG-12 | 533 | 8.1 | Roman Catholic |
| Stars School | 21.8 |
Special education | Ungraded-Ungraded | 10 | 10.0 | Nonsectarian |
| Stars School | 21.8 |
Special education | Ungraded-Ungraded | 10 | 10.0 | Nonsectarian |
| Contra Costa Christian School | 21.8 |
Regular elementary or secondary | Pre-KG-12 | 339 | 11.7 | Christian (no specific denomination) |
| Woodside Hills Christian Academy | 22.1 |
Regular elementary or secondary | Pre-KG-12 | 81 | 8.3 | Baptist |
| Pleasant Hill Adventist Academy | 22.4 |
Regular elementary or secondary | KG-12 | 252 | 16.1 | Seventh-Day Adventist |
| Wherry Academy | 22.6 |
Special program emphasis | 5-10 | 3 | 3.0 | Nonsectarian |
| Spectrum Center - Mission Valley | 23.6 |
Special education | Ungraded-Ungraded | 45 | 9.0 | Nonsectarian |
| Union City Christian Academy | 23.8 |
Regular elementary or secondary | KG-12 | 75 | 6.4 | Pentecostal |
| Sacred Heart Schools Atherton | 24.4 |
Regular elementary or secondary | Pre-KG-12 | 977 | 9.3 | Roman Catholic |
| New Vistas Christian School | 24.6 |
Special education | 6-12 | 30 | 7.5 | Christian (no specific denomination) |
| Spectrum Center - Valley | 24.9 |
Special education | Ungraded-Ungraded | 56 | 8.0 | Nonsectarian |
| North Bay Christian Academy | 25.0 |
Regular elementary or secondary | KG-12 | 84 | 9.8 | Christian (no specific denomination) |
