| Alma Heights Christian Academy | 0.0 |
Regular elementary or secondary | KG-12 | 295 | 12.0 | Other |
| Highlands Christian Schools | 3.4 |
Regular elementary or secondary | Pre-KG-12 | 613 | 17.3 | Christian (no specific denomination) |
| Wings Learning Center | 5.8 |
Special education | Ungraded-Ungraded | 17 | 5.7 | Nonsectarian |
| Roger Williams Academy | 6.3 |
Regular elementary or secondary | 1-12 | 25 | 8.1 | Baptist |
| San Francisco Christian School | 8.8 |
Regular elementary or secondary | Pre-KG-12 | 224 | 14.0 | Baptist |
| Crystal Springs Uplands School | 8.8 |
Regular elementary or secondary | 6-12 | 350 | 6.6 | Nonsectarian |
| Stanbridge Academy | 9.0 |
Special education | Ungraded-Ungraded | 93 | 4.9 | Nonsectarian |
| Sr Martin College Preparatory School | 10.1 |
Regular elementary or secondary | 6-12 | 29 | 7.6 | Other |
| Cornerstone Academy | 10.6 |
Regular elementary or secondary | Pre-KG-12 | 1058 | 13.6 | Baptist |
| Alpha Beacon Christian School | 11.3 |
Regular elementary or secondary | Pre-KG-12 | 152 | 11.9 | Christian (no specific denomination) |
| Lycee Francais La Perouse - San Francisco Campus | 11.4 |
Special program emphasis | Pre-KG-12 | 864 | 24.0 | Nonsectarian |
| Joshua Marie Cameron Academy | 12.1 |
Special education | 6-12 | 12 | 6.0 | Nonsectarian |
| Sand Paths Academy | 12.2 |
Special education | 6-12 | 26 | 4.9 | Nonsectarian |
| Rise Institute | 12.5 |
Special education | 4-12 | 44 | 14.7 | Nonsectarian |
| Erikson School | 13.0 |
Special education | 4-12 | 21 | 7.0 | Nonsectarian |
| Lisa Kampner Hebrew Academy | 13.1 |
Regular elementary or secondary | Pre-KG-12 | 132 | 6.7 | Jewish |
| St John Of San Francisco Orthodox Academy | 13.3 |
Regular elementary or secondary | KG-12 | 48 | 3.7 | Other |
| San Francisco Waldorf School | 14.3 |
Special program emphasis | KG-12 | 407 | 10.3 | Nonsectarian |
| Sterne School | 14.4 |
Special education | 6-12 | 50 | 4.4 | Nonsectarian |
| West Bay High | 14.9 |
Regular elementary or secondary | Ungraded-Ungraded | 49 | 12.9 | Nonsectarian |
| Hergl School | 15.2 |
Special education | Ungraded-Ungraded | 8 | 8.0 | Nonsectarian |
| Woodside Hills Christian Academy | 16.2 |
Regular elementary or secondary | Pre-KG-12 | 81 | 8.3 | Baptist |
| Wherry Academy | 17.8 |
Special program emphasis | 5-10 | 3 | 3.0 | Nonsectarian |
| Children's Learning Center | 18.2 |
Special education | KG-12 | 72 | 7.1 | Nonsectarian |
| Children's Learning Center | 18.2 |
Special education | Ungraded-Ungraded | 23 | 5.8 | Nonsectarian |
| Pentecostal Way Of Truth Academy | 18.5 |
Regular elementary or secondary | KG-12 | 15 | 1.6 | Nonsectarian |
| Sacred Heart Schools Atherton | 19.0 |
Regular elementary or secondary | Pre-KG-12 | 977 | 9.3 | Roman Catholic |
| Oak Hill School | 19.5 |
Special education | 1-12 | 20 | 5.0 | Nonsectarian |
| Agnes Memorial Christian Academy | 19.6 |
Regular elementary or secondary | Pre-KG-12 | 15 | 3.8 | Pentecostal |
| Asa Academy | 19.8 |
Regular elementary or secondary | 6-12 | 49 | 3.4 | Nonsectarian |
| St Andrew Missionary Baptist Church Pvt School | 19.9 |
Special program emphasis | KG-10 | 45 | 22.5 | Baptist |
| Esther B Clark School-childrens Health Council | 20.1 |
Special education | 4-10 | 50 | 4.6 | Nonsectarian |
| Clara Mohammed School | 20.1 |
Regular elementary or secondary | KG-12 | 27 | 5.1 | Islamic |
| Patten Academy Of Christian Education | 20.3 |
Regular elementary or secondary | KG-12 | 197 | 12.2 | Christian (no specific denomination) |
| Chinese Christian Schools | 20.5 |
Special program emphasis | KG-12 | 915 | 11.0 | Christian (no specific denomination) |
| Community Christian School | 20.8 |
Regular elementary or secondary | KG-12 | 147 | 11.3 | Assembly of God |
| Woodside Priory School | 21.2 |
Regular elementary or secondary | 6-12 | 356 | 7.4 | Roman Catholic |
| The Renaissance School | 21.3 |
Montessori | Ungraded-Ungraded | 147 | 6.1 | Nonsectarian |
| Candell's College Preparatory Academy | 21.4 |
Regular elementary or secondary | KG-12 | 60 | 13.6 | Christian (no specific denomination) |
| Castilleja School | 21.4 |
Regular elementary or secondary | 6-12 | 415 | 8.0 | Nonsectarian |
| Eastside College Preparatory School | 21.6 |
Regular elementary or secondary | 6-12 | 222 | 9.2 | Nonsectarian |
| Via Center | 22.1 |
Special education | Ungraded-Ungraded | 18 | 9.0 | Nonsectarian |
| International Bible Baptist Academy | 22.1 |
Regular elementary or secondary | KG-12 | 39 | 4.4 | Baptist |
| Seneca Center | 22.5 |
Special education | 1-12 | 113 | 9.7 | Nonsectarian |
| Beyt Hasepher | 22.7 |
Alternative/other | 1-12 | 19 | 2.4 | Christian (no specific denomination) |
| Bowman International School | 23.8 |
Montessori | Ungraded-Ungraded | 194 | 7.5 | Nonsectarian |
| Achievekids | 23.9 |
Special education | 4-12 | 47 | 6.7 | Nonsectarian |
