| Lighthouse Christian Academy | 2.6 |
Regular elementary or secondary | KG-12 | 120 | 8.2 | Baptist |
| Dunamis Learning Center | 3.0 |
Regular elementary or secondary | 6-12 | 8 | 4.2 | Christian (no specific denomination) |
| La Mesa Christian School | 3.2 |
Regular elementary or secondary | Pre-KG-12 | 63 | 7.3 | Baptist |
| Rainbow Christian | 3.2 |
Regular elementary or secondary | 3-12 | 6 | 6.0 | Christian (no specific denomination) |
| True Faith Academy | 3.3 |
Regular elementary or secondary | 1-12 | 24 | 12.0 | Christian (no specific denomination) |
| Kuyper Preparatory School | 3.7 |
Regular elementary or secondary | KG-12 | 126 | 11.2 | Christian (no specific denomination) |
| Springall Academy | 4.4 |
Special education | 2-12 | 71 | 7.1 | Nonsectarian |
| Del Rey Schools | 4.9 |
Alternative/other | KG-12 | 28 | 2.2 | Other |
| Tabernacle Christian Academy | 5.6 |
Regular elementary or secondary | Pre-KG-12 | 75 | 8.5 | Pentecostal |
| San Diego Academy | 6.5 |
Regular elementary or secondary | KG-12 | 333 | 15.9 | Seventh-Day Adventist |
| Home School Alternative, The | 6.5 |
Regular elementary or secondary | 2-10 | 8 | 4.0 | Christian (no specific denomination) |
| Excelsior Academy | 6.7 |
Regular elementary or secondary | 6-12 | 63 | 4.5 | Nonsectarian |
| Faithful Ambassadors Bible | 7.0 |
Regular elementary or secondary | KG-12 | 117 | 11.7 | Baptist |
| Sam & Rose Stein Education Center | 7.0 |
Special education | Ungraded-Ungraded | 189 | 8.5 | Nonsectarian |
| Calvary Christian Jr/sr High School | 7.5 |
Regular elementary or secondary | Pre-KG-12 | 465 | 11.6 | Christian (no specific denomination) |
| Calvary Christian Academy | 7.5 |
Regular elementary or secondary | Pre-KG-12 | 400 | 15.4 | Christian (no specific denomination) |
| South Bay Christian Academy | 8.6 |
Regular elementary or secondary | KG-12 | 42 | 7.0 | Pentecostal |
| Marjorie Cook Education Center | 9.1 |
Special education | 1-12 | 110 | 5.2 | Nonsectarian |
| Sam & Rose Stein Education Center | 9.3 |
Special education | 4-12 | 62 | 15.5 | Nonsectarian |
| Aseltine School | 9.3 |
Special education | 5-12 | 49 | 16.3 | Nonsectarian |
| Balboa City School | 10.0 |
Special education | 1-12 | 95 | 6.1 | Nonsectarian |
| Otay Christian Academy | 10.8 |
Regular elementary or secondary | KG-12 | 37 | 14.2 | Other |
| Heritage Christian School | 10.8 |
Regular elementary or secondary | KG-12 | 868 | 15.2 | Christian (no specific denomination) |
| Midway Baptist School | 12.1 |
Regular elementary or secondary | KG-12 | 342 | 15.1 | Baptist |
| New Life Christian Academy | 13.2 |
Regular elementary or secondary | Pre-KG-12 | 51 | 10.2 | Christian (no specific denomination) |
| Rock Academy, The | 13.5 |
Regular elementary or secondary | Pre-KG-12 | 244 | 14.0 | Christian (no specific denomination) |
| Sierra Schools Of California | 13.9 |
Special education | 1-12 | 39 | 7.8 | Nonsectarian |
| Horizon Elementary School | 14.1 |
Regular elementary or secondary | Pre-KG-12 | 842 | 13.6 | Christian (no specific denomination) |
| La Jolla Country Day School | 16.3 |
Regular elementary or secondary | Pre-KG-12 | 973 | 9.5 | Nonsectarian |
| San Diego Jewish Academy | 19.4 |
Regular elementary or secondary | KG-12 | 622 | 12.8 | Jewish |
| Maranatha Christian School | 21.5 |
Regular elementary or secondary | Pre-KG-11 | 504 | 13.7 | Other |
| Winston School | 21.7 |
Special education | 5-12 | 100 | 7.7 | Nonsectarian |
| Santa Fe Montessori School | 23.2 |
Montessori | Ungraded-Ungraded | 200 | 11.8 | Nonsectarian |
| Cal Coast Academy | 23.4 |
Regular elementary or secondary | 6-12 | 24 | 2.3 | Nonsectarian |
| Santa Fe Christian Schools | 23.4 |
Regular elementary or secondary | Pre-KG-12 | 986 | 12.4 | Christian (no specific denomination) |
| Tecate Christian School | 23.7 |
Regular elementary or secondary | 1-12 | 95 | 12.2 | Christian (no specific denomination) |
| Encinitas Country Day School | 24.9 |
Montessori | Pre-KG-9 | 249 | 7.5 | Nonsectarian |
