| Escondido Apostolic Christian Academy | 1.7 |
Regular elementary or secondary | KG-12 | 55 | 5.5 | Other |
| Sierra Madre Academy | 6.0 |
Regular elementary or secondary | KG-12 | 223 | 14.3 | Roman Catholic |
| Cchat Center | 6.3 |
Special education | Pre-KG-Pre-KG | 3 | 3.0 | Nonsectarian |
| West Coast Baptist School | 9.1 |
Regular elementary or secondary | Pre-KG-12 | 44 | 13.3 | Baptist |
| Maranatha Christian School | 9.5 |
Regular elementary or secondary | Pre-KG-11 | 504 | 13.7 | Other |
| New Haven Nps | 9.9 |
Special education | 6-12 | 84 | 10.5 | Nonsectarian |
| Tri-city Christian Schools | 11.2 |
Regular elementary or secondary | Pre-KG-12 | 989 | 14.6 | Baptist |
| The Grauer School | 12.8 |
Regular elementary or secondary | 6-12 | 121 | 4.2 | Nonsectarian |
| Encinitas Country Day School | 13.1 |
Montessori | Pre-KG-9 | 249 | 7.5 | Nonsectarian |
| Cal Coast Academy | 14.3 |
Regular elementary or secondary | 6-12 | 24 | 2.3 | Nonsectarian |
| Santa Fe Montessori School | 14.6 |
Montessori | Ungraded-Ungraded | 200 | 11.8 | Nonsectarian |
| Aswe-t Pati'a Christian Academy | 14.7 |
Alternative/other | KG-12 | 27 | 8.2 | Christian (no specific denomination) |
| Santa Fe Christian Schools | 14.8 |
Regular elementary or secondary | Pre-KG-12 | 986 | 12.4 | Christian (no specific denomination) |
| Teri Learning Academy | 15.6 |
Special education | Ungraded-Ungraded | 56 | 11.2 | Nonsectarian |
| Sierra Schools Of California | 16.7 |
Special education | 1-12 | 39 | 7.8 | Nonsectarian |
| San Diego Jewish Academy | 17.0 |
Regular elementary or secondary | KG-12 | 622 | 12.8 | Jewish |
| Winston School | 17.1 |
Special education | 5-12 | 100 | 7.7 | Nonsectarian |
| La Jolla Country Day School | 20.2 |
Regular elementary or secondary | Pre-KG-12 | 973 | 9.5 | Nonsectarian |
| Heritage Christian School | 21.9 |
Regular elementary or secondary | KG-12 | 868 | 15.2 | Christian (no specific denomination) |
| Horizon Elementary School | 23.7 |
Regular elementary or secondary | Pre-KG-12 | 842 | 13.6 | Christian (no specific denomination) |
| Linfield Christian School | 24.1 |
Regular elementary or secondary | KG-12 | 896 | 17.3 | Christian (no specific denomination) |
| Excelsior Academy | 24.3 |
Regular elementary or secondary | 6-12 | 63 | 4.5 | Nonsectarian |
| Springall Academy | 24.8 |
Special education | 2-12 | 71 | 7.1 | Nonsectarian |
