| Roger Williams Academy | 2.9 |
Regular elementary or secondary | 1-12 | 25 | 8.1 | Baptist |
| Alma Heights Christian Academy | 3.4 |
Regular elementary or secondary | KG-12 | 295 | 12.0 | Other |
| Wings Learning Center | 3.9 |
Special education | Ungraded-Ungraded | 17 | 5.7 | Nonsectarian |
| San Francisco Christian School | 6.1 |
Regular elementary or secondary | Pre-KG-12 | 224 | 14.0 | Baptist |
| Sr Martin College Preparatory School | 6.8 |
Regular elementary or secondary | 6-12 | 29 | 7.6 | Other |
| Stanbridge Academy | 7.2 |
Special education | Ungraded-Ungraded | 93 | 4.9 | Nonsectarian |
| Crystal Springs Uplands School | 7.6 |
Regular elementary or secondary | 6-12 | 350 | 6.6 | Nonsectarian |
| Cornerstone Academy | 7.6 |
Regular elementary or secondary | Pre-KG-12 | 1058 | 13.6 | Baptist |
| Joshua Marie Cameron Academy | 8.9 |
Special education | 6-12 | 12 | 6.0 | Nonsectarian |
| Lycee Francais La Perouse - San Francisco Campus | 9.1 |
Special program emphasis | Pre-KG-12 | 864 | 24.0 | Nonsectarian |
| Sand Paths Academy | 9.3 |
Special education | 6-12 | 26 | 4.9 | Nonsectarian |
| Rise Institute | 9.3 |
Special education | 4-12 | 44 | 14.7 | Nonsectarian |
| Alpha Beacon Christian School | 10.4 |
Regular elementary or secondary | Pre-KG-12 | 152 | 11.9 | Christian (no specific denomination) |
| Lisa Kampner Hebrew Academy | 10.7 |
Regular elementary or secondary | Pre-KG-12 | 132 | 6.7 | Jewish |
| Erikson School | 10.8 |
Special education | 4-12 | 21 | 7.0 | Nonsectarian |
| St John Of San Francisco Orthodox Academy | 11.1 |
Regular elementary or secondary | KG-12 | 48 | 3.7 | Other |
| San Francisco Waldorf School | 11.7 |
Special program emphasis | KG-12 | 407 | 10.3 | Nonsectarian |
| Sterne School | 11.8 |
Special education | 6-12 | 50 | 4.4 | Nonsectarian |
| Hergl School | 12.4 |
Special education | Ungraded-Ungraded | 8 | 8.0 | Nonsectarian |
| West Bay High | 14.0 |
Regular elementary or secondary | Ungraded-Ungraded | 49 | 12.9 | Nonsectarian |
| Children's Learning Center | 14.7 |
Special education | KG-12 | 72 | 7.1 | Nonsectarian |
| Children's Learning Center | 14.8 |
Special education | Ungraded-Ungraded | 23 | 5.8 | Nonsectarian |
| Pentecostal Way Of Truth Academy | 15.1 |
Regular elementary or secondary | KG-12 | 15 | 1.6 | Nonsectarian |
| Woodside Hills Christian Academy | 15.6 |
Regular elementary or secondary | Pre-KG-12 | 81 | 8.3 | Baptist |
| Agnes Memorial Christian Academy | 16.1 |
Regular elementary or secondary | Pre-KG-12 | 15 | 3.8 | Pentecostal |
| Asa Academy | 16.4 |
Regular elementary or secondary | 6-12 | 49 | 3.4 | Nonsectarian |
| St Andrew Missionary Baptist Church Pvt School | 16.5 |
Special program emphasis | KG-10 | 45 | 22.5 | Baptist |
| Clara Mohammed School | 16.7 |
Regular elementary or secondary | KG-12 | 27 | 5.1 | Islamic |
| Wherry Academy | 16.9 |
Special program emphasis | 5-10 | 3 | 3.0 | Nonsectarian |
| Patten Academy Of Christian Education | 16.9 |
Regular elementary or secondary | KG-12 | 197 | 12.2 | Christian (no specific denomination) |
| Chinese Christian Schools | 17.4 |
Special program emphasis | KG-12 | 915 | 11.0 | Christian (no specific denomination) |
| Oak Hill School | 17.4 |
Special education | 1-12 | 20 | 5.0 | Nonsectarian |
| Community Christian School | 17.7 |
Regular elementary or secondary | KG-12 | 147 | 11.3 | Assembly of God |
| The Renaissance School | 17.8 |
Montessori | Ungraded-Ungraded | 147 | 6.1 | Nonsectarian |
| Candell's College Preparatory Academy | 18.0 |
Regular elementary or secondary | KG-12 | 60 | 13.6 | Christian (no specific denomination) |
| Sacred Heart Schools Atherton | 18.4 |
Regular elementary or secondary | Pre-KG-12 | 977 | 9.3 | Roman Catholic |
| Via Center | 18.8 |
Special education | Ungraded-Ungraded | 18 | 9.0 | Nonsectarian |
| International Bible Baptist Academy | 18.9 |
Regular elementary or secondary | KG-12 | 39 | 4.4 | Baptist |
| Seneca Center | 19.4 |
Special education | 1-12 | 113 | 9.7 | Nonsectarian |
| Esther B Clark School-childrens Health Council | 19.4 |
Special education | 4-10 | 50 | 4.6 | Nonsectarian |
| Beyt Hasepher | 19.5 |
Alternative/other | 1-12 | 19 | 2.4 | Christian (no specific denomination) |
| Eastside College Preparatory School | 20.5 |
Regular elementary or secondary | 6-12 | 222 | 9.2 | Nonsectarian |
| Castilleja School | 20.6 |
Regular elementary or secondary | 6-12 | 415 | 8.0 | Nonsectarian |
| Woodside Priory School | 21.3 |
Regular elementary or secondary | 6-12 | 356 | 7.4 | Roman Catholic |
| Elim Christian School/colegio Evangelico Elim | 22.1 |
Regular elementary or secondary | KG-12 | 44 | 7.3 | Christian (no specific denomination) |
| Family Christian Academy | 22.2 |
Regular elementary or secondary | Pre-KG-12 | 7 | 3.9 | Pentecostal |
| Union City Christian Academy | 22.8 |
Regular elementary or secondary | KG-12 | 75 | 6.4 | Pentecostal |
| Achievekids | 23.1 |
Special education | 4-12 | 47 | 6.7 | Nonsectarian |
| Spectrum Center - Mission Valley | 23.1 |
Special education | Ungraded-Ungraded | 45 | 9.0 | Nonsectarian |
| Bowman International School | 23.2 |
Montessori | Ungraded-Ungraded | 194 | 7.5 | Nonsectarian |
| Arlington Christian School | 23.3 |
Regular elementary or secondary | KG-12 | 49 | 9.2 | Baptist |
| King's Academy | 23.5 |
Regular elementary or secondary | 1-12 | 42 | 1.7 | Christian (no specific denomination) |
| Fremont Christian School | 24.0 |
Regular elementary or secondary | Pre-KG-12 | 1100 | 20.9 | Assembly of God |
| Stinson Beach Montessori School | 24.9 |
Montessori | Ungraded-Ungraded | 1 | 1.0 | Nonsectarian |
