| Achievekids | 2.9 |
Special education | 4-12 | 47 | 6.7 | Nonsectarian |
| The King's Academy | 3.0 |
Regular elementary or secondary | 6-12 | 849 | 14.4 | Christian (no specific denomination) |
| Bowman International School | 3.4 |
Montessori | Ungraded-Ungraded | 194 | 7.5 | Nonsectarian |
| Waldorf School Of The Peninsula | 4.1 |
Special program emphasis | Pre-KG-9 | 242 | 12.8 | Nonsectarian |
| School Of Choise | 5.1 |
Regular elementary or secondary | 6-12 | 22 | 3.5 | Other |
| Castilleja School | 5.5 |
Regular elementary or secondary | 6-12 | 415 | 8.0 | Nonsectarian |
| Eastside College Preparatory School | 5.8 |
Regular elementary or secondary | 6-12 | 222 | 9.2 | Nonsectarian |
| Cedarwood Sudbury School | 6.0 |
Special program emphasis | 1-12 | 10 | 3.3 | Nonsectarian |
| North Valley Baptist School | 6.3 |
Regular elementary or secondary | KG-12 | 241 | 16.9 | Baptist |
| Esther B Clark School-childrens Health Council | 6.8 |
Special education | 4-10 | 50 | 4.6 | Nonsectarian |
| Sierra Elementary And High School | 6.9 |
Regular elementary or secondary | KG-12 | 90 | 10.7 | Nonsectarian |
| Sacred Heart Schools Atherton | 7.8 |
Regular elementary or secondary | Pre-KG-12 | 977 | 9.3 | Roman Catholic |
| Pacific Autism Center For Education | 7.9 |
Special education | Ungraded-Ungraded | 50 | 7.1 | Nonsectarian |
| Morgan Autism Center | 8.2 |
Special education | Ungraded-Ungraded | 53 | 4.8 | Nonsectarian |
| Beginning Steps To Independence Inc | 8.3 |
Special education | Ungraded-Ungraded | 28 | 14.0 | Nonsectarian |
| Woodside Priory School | 8.3 |
Regular elementary or secondary | 6-12 | 356 | 7.4 | Roman Catholic |
| Wherry Academy | 9.1 |
Special program emphasis | 5-10 | 3 | 3.0 | Nonsectarian |
| Veritas Christian Academy | 9.4 |
Regular elementary or secondary | KG-12 | 47 | 6.6 | Calvinist |
| Woodside Hills Christian Academy | 10.7 |
Regular elementary or secondary | Pre-KG-12 | 81 | 8.3 | Baptist |
| Fremont Christian School | 10.9 |
Regular elementary or secondary | Pre-KG-12 | 1100 | 20.9 | Assembly of God |
| Seneca Center | 11.0 |
Special education | Ungraded-Ungraded | 61 | 10.2 | Nonsectarian |
| Willow Vale Christian Children's Center | 11.8 |
Regular elementary or secondary | Pre-KG-12 | 86 | 8.3 | Methodist |
| West Bay High | 12.0 |
Regular elementary or secondary | Ungraded-Ungraded | 49 | 12.9 | Nonsectarian |
| Montessori School Of Fremont | 12.2 |
Montessori | Ungraded-Ungraded | 230 | 25.6 | Nonsectarian |
| Union City Christian Academy | 13.4 |
Regular elementary or secondary | KG-12 | 75 | 6.4 | Pentecostal |
| White Road Baptist Academy | 13.6 |
Regular elementary or secondary | 3-12 | 16 | 4.6 | Baptist |
| Our Shepherd's Academy | 13.8 |
Regular elementary or secondary | 2-11 | 7 | 1.8 | Christian (no specific denomination) |
| Achieve Kids | 13.8 |
Special education | Ungraded-Ungraded | 50 | 5.6 | Nonsectarian |
| Pine Hill School | 13.9 |
Special education | 2-12 | 64 | 8.0 | Nonsectarian |
| Live Oak Academy | 14.2 |
Alternative/other | KG-11 | 99 | 14.1 | Christian (no specific denomination) |
| St Thomas More School | 14.4 |
Regular elementary or secondary | KG-12 | 193 | 16.9 | Roman Catholic |
| Spectrum Center - Mission Valley | 14.5 |
Special education | Ungraded-Ungraded | 45 | 9.0 | Nonsectarian |
| Liberty Baptist School | 14.8 |
Regular elementary or secondary | Pre-KG-12 | 236 | 13.4 | Baptist |
| Alpha Beacon Christian School | 15.7 |
Regular elementary or secondary | Pre-KG-12 | 152 | 11.9 | Christian (no specific denomination) |
| Valley Christian High | 15.7 |
Regular elementary or secondary | KG-12 | 2200 | 18.6 | Christian (no specific denomination) |
| Crystal Springs Uplands School | 18.5 |
Regular elementary or secondary | 6-12 | 350 | 6.6 | Nonsectarian |
| Stanbridge Academy | 18.9 |
Special education | Ungraded-Ungraded | 93 | 4.9 | Nonsectarian |
| Community Christian School | 20.2 |
Regular elementary or secondary | KG-12 | 147 | 11.3 | Assembly of God |
| Chinese Christian Schools | 20.4 |
Special program emphasis | KG-12 | 915 | 11.0 | Christian (no specific denomination) |
| Lighthouse Baptist School | 20.9 |
Regular elementary or secondary | KG-11 | 19 | 5.8 | Baptist |
| International Bible Baptist Academy | 21.1 |
Regular elementary or secondary | KG-12 | 39 | 4.4 | Baptist |
| Seneca Center | 21.6 |
Special education | 1-12 | 113 | 9.7 | Nonsectarian |
| Valley Christian Jr/sr High School | 21.6 |
Regular elementary or secondary | Pre-KG-12 | 965 | 16.2 | Christian (no specific denomination) |
| Wings Learning Center | 22.1 |
Special education | Ungraded-Ungraded | 17 | 5.7 | Nonsectarian |
| St Lawrence Academy | 24.1 |
Regular elementary or secondary | KG-12 | 48 | 12.0 | Other |
