| San Diego Christian Academy | 2.0 |
Regular elementary or secondary | 7-12 | 24 | 10.4 | Christian (no specific denomination) |
| Crenshaw Booker T Christian School | 2.4 |
Regular elementary or secondary | 9-12 | 10 | 5.0 | Baptist |
| Lutheran High Of San Diego | 2.7 |
Regular elementary or secondary | 9-12 | 89 | 10.5 | Lutheran Church - Missouri Synod |
| St Augustine High School | 3.4 |
Regular elementary or secondary | 9-12 | 729 | 14.1 | Roman Catholic |
| Academy Of Our Lady Of Peace | 5.5 |
Regular elementary or secondary | 9-12 | 740 | 18.6 | Roman Catholic |
| Creative Learning Academy, The | 8.5 |
Special education | 8-12 | 22 | 11.0 | Nonsectarian |
| Foothills Christian High School | 8.8 |
Regular elementary or secondary | 9-12 | 234 | 15.1 | Christian (no specific denomination) |
| Horizon Jr & Sr High School | 10.0 |
Regular elementary or secondary | 7-12 | 492 | 12.4 | Christian (no specific denomination) |
| Christian Jr/sr High School | 12.8 |
Regular elementary or secondary | 7-12 | 643 | 13.5 | Baptist |
| Fred Finch Youth Center | 13.4 |
Special education | 10-12 | 10 | 5.0 | Nonsectarian |
| Torah High Schools Of San Diego | 13.8 |
Regular elementary or secondary | 9-12 | 33 | 1.5 | Jewish |
| Southern Calif Yeshiva High School | 14.6 |
Regular elementary or secondary | 9-12 | 31 | 3.9 | Jewish |
| The Bishop's School | 15.0 |
Regular elementary or secondary | 7-12 | 742 | 9.8 | Episcopal |
