| Mountain Empire Unified School District | 2013 API | 2012 API |
| College Preparatory Middle | 941 | 924 |
| Descanso Elementary | 900 | 844 |
| Jacumba Middle | 811 | B |
| San Diego Neighborhood Homeschools | 802 | 805 |
| Clover Flat Elementary | 800 | 809 |
| Mountain Peak Charter | 796 | 770 |
| Pine Valley Middle | 766 | B |
| Campo Elementary | 694 | 725 |
| Mountain Empire High | 683 | 674 |
| Potrero Elementary | 676 | 696 |
| California Pacific Charter School of San Diego | 653 | 651 |
| San Diego Virtual | 632 | 654 |
| Pivot Charter School - San Diego | 629 | 701 |
| Academy of Arts and Sciences: Del Mar Elementary (K-5) | | |
| Academy of Arts and Sciences: Del Mar Middle & High (6-12) | | |
| Academy of Arts and Sciences: El Cajon Middle and High (6-12) | | |
| Campo High (Continuation) | | |
| Cottonwood Community Day | | |
| Hillside Junior/Senior High | | |
| Save our Future | | |