| Tri-city Christian Schools | 4.4 |
Regular elementary or secondary | Pre-KG-12 | 989 | 14.6 | Baptist |
| New Haven Nps | 6.0 |
Special education | 6-12 | 84 | 10.5 | Nonsectarian |
| West Coast Baptist School | 6.8 |
Regular elementary or secondary | Pre-KG-12 | 44 | 13.3 | Baptist |
| Sierra Madre Academy | 10.1 |
Regular elementary or secondary | KG-12 | 223 | 14.3 | Roman Catholic |
| Cchat Center | 10.1 |
Special education | Pre-KG-Pre-KG | 3 | 3.0 | Nonsectarian |
| The Grauer School | 14.1 |
Regular elementary or secondary | 6-12 | 121 | 4.2 | Nonsectarian |
| Encinitas Country Day School | 14.5 |
Montessori | Pre-KG-9 | 249 | 7.5 | Nonsectarian |
| Calvin Christian School Of Escondido/preschool | 15.6 |
Regular elementary or secondary | Pre-KG-12 | 479 | 15.4 | Calvinist |
| Cal Coast Academy | 16.3 |
Regular elementary or secondary | 6-12 | 24 | 2.3 | Nonsectarian |
| Santa Fe Christian Schools | 16.5 |
Regular elementary or secondary | Pre-KG-12 | 986 | 12.4 | Christian (no specific denomination) |
| Santa Fe Montessori School | 16.6 |
Montessori | Ungraded-Ungraded | 200 | 11.8 | Nonsectarian |
| Escondido Apostolic Christian Academy | 17.3 |
Regular elementary or secondary | KG-12 | 55 | 5.5 | Other |
| Maranatha Christian School | 18.0 |
Regular elementary or secondary | Pre-KG-11 | 504 | 13.7 | Other |
| Aswe-t Pati'a Christian Academy | 18.5 |
Alternative/other | KG-12 | 27 | 8.2 | Christian (no specific denomination) |
| Winston School | 18.9 |
Special education | 5-12 | 100 | 7.7 | Nonsectarian |
| San Diego Jewish Academy | 20.7 |
Regular elementary or secondary | KG-12 | 622 | 12.8 | Jewish |
| Talega Preparatory Academy | 21.3 |
Alternative/other | KG-12 | 39 | 39.0 | Nonsectarian |
| St Michael's Academy | 21.4 |
Regular elementary or secondary | Pre-KG-12 | 134 | 14.9 | Episcopal |
| Linfield Christian School | 24.2 |
Regular elementary or secondary | KG-12 | 896 | 17.3 | Christian (no specific denomination) |
| La Jolla Country Day School | 24.6 |
Regular elementary or secondary | Pre-KG-12 | 973 | 9.5 | Nonsectarian |
