| Foothills Christian High School | 4.7 |
Regular elementary or secondary | 9-12 | 234 | 15.1 | Christian (no specific denomination) |
| Christian Jr/sr High School | 5.1 |
Regular elementary or secondary | 7-12 | 643 | 13.5 | Baptist |
| Lutheran High Of San Diego | 11.0 |
Regular elementary or secondary | 9-12 | 89 | 10.5 | Lutheran Church - Missouri Synod |
| Academy Of Our Lady Of Peace | 12.1 |
Regular elementary or secondary | 9-12 | 740 | 18.6 | Roman Catholic |
| Creative Learning Academy, The | 12.6 |
Special education | 8-12 | 22 | 11.0 | Nonsectarian |
| St Augustine High School | 12.9 |
Regular elementary or secondary | 9-12 | 729 | 14.1 | Roman Catholic |
| Horizon Jr & Sr High School | 13.3 |
Regular elementary or secondary | 7-12 | 492 | 12.4 | Christian (no specific denomination) |
| Emmanuel Arts Academy | 13.4 |
Regular elementary or secondary | 8-12 | 13 | 5.0 | Other |
| Keystone Academy | 13.5 |
Special education | 9-11 | 18 | 9.0 | Nonsectarian |
| Torah High Schools Of San Diego | 14.4 |
Regular elementary or secondary | 9-12 | 33 | 1.5 | Jewish |
| Crenshaw Booker T Christian School | 14.6 |
Regular elementary or secondary | 9-12 | 10 | 5.0 | Baptist |
| San Diego Christian Academy | 14.8 |
Regular elementary or secondary | 7-12 | 24 | 10.4 | Christian (no specific denomination) |
| Southern Calif Yeshiva High School | 16.1 |
Regular elementary or secondary | 9-12 | 31 | 3.9 | Jewish |
| The Bishop's School | 18.6 |
Regular elementary or secondary | 7-12 | 742 | 9.8 | Episcopal |
| Summerhill School | 19.6 |
Special education | 9-12 | 9 | 4.7 | Nonsectarian |
| Pacific Academy | 22.6 |
Regular elementary or secondary | 7-12 | 23 | 4.6 | Nonsectarian |
| Julian Youth Academy | 24.5 |
Alternative/other | 8-12 | 46 | 2.6 | Christian (no specific denomination) |
