| Alpine Christian | 0.0 |
Regular elementary or secondary | KG-8 | 30 | 6.8 | Christian (no specific denomination) |
| Foothills Christian Elementary School | 8.2 |
Alternative/other | KG-8 | 210 | 28.4 | Christian (no specific denomination) |
| Meridian Christian Elementary | 8.4 |
Regular elementary or secondary | KG-6 | 176 | 16.8 | Baptist |
| Our Lady Of Perpetual Help School | 8.4 |
Regular elementary or secondary | KG-8 | 184 | 13.6 | Roman Catholic |
| El Cajon Seventh-day Adventist | 9.3 |
Regular elementary or secondary | KG-8 | 43 | 14.3 | Seventh-Day Adventist |
| St Kieran School | 9.5 |
Regular elementary or secondary | KG-8 | 176 | 15.2 | Roman Catholic |
| Pepper Valley Learning Center | 9.6 |
Early childhood program/child care center | Pre-KG-KG | 8 | 8.0 | Nonsectarian |
| Taproot Montessori Preschool & Kindergarten | 9.7 |
Montessori | Pre-KG-KG | 6 | 6.0 | Nonsectarian |
| Bostonia Christian Elementary School | 9.8 |
Regular elementary or secondary | KG-6 | 111 | 13.1 | Baptist |
| Childrens Creative & Performing Arts Academy | 10.2 |
Montessori | Pre-KG-5 | 40 | 5.9 | Nonsectarian |
| Taproot Montessori Preschool & Kindergarten | 10.4 |
Montessori | Pre-KG-KG | 9 | 5.6 | Nonsectarian |
| Holy Trinity Elementary School | 10.6 |
Regular elementary or secondary | Pre-KG-8 | 224 | 19.6 | Roman Catholic |
| Chase Ranch Montessori School | 11.2 |
Montessori | Pre-KG-Trans. KG | 12 | 3.5 | Nonsectarian |
| First Lutheran Preschool & Kindergarten | 11.4 |
Early childhood program/child care center | Pre-KG-KG | 7 | 7.8 | Lutheran Church - Missouri Synod |
| Montessori Achievement Centre | 13.3 |
Montessori | Pre-KG-Trans. KG | 6 | 2.0 | Nonsectarian |
| St Ephrem Maronite Catholic Academy | 13.9 |
Regular elementary or secondary | KG-8 | 25 | 5.2 | Other |
| Mt Helix Academy | 13.9 |
Regular elementary or secondary | KG-8 | 229 | 10.9 | Nonsectarian |
| Our Lady Of Grace Elem School | 13.9 |
Regular elementary or secondary | KG-8 | 262 | 17.7 | Roman Catholic |
| Shepherd Of The Hills Lutheran School | 14.0 |
Regular elementary or secondary | KG-7 | 31 | 15.5 | Wisconsin Evangelical Lutheran Synod |
| Helix Montessori School | 14.1 |
Montessori | Pre-KG-KG | 1 | 1.0 | Nonsectarian |
| Santa Sophia Academy | 14.2 |
Regular elementary or secondary | KG-8 | 218 | 19.3 | Roman Catholic |
| Warren-walker School-la Mesa | 14.6 |
Regular elementary or secondary | Pre-KG-3 | 88 | 7.5 | Nonsectarian |
| Trinity Christian School | 15.1 |
Regular elementary or secondary | Pre-KG-8 | 162 | 17.4 | Presbyterian |
| Montessori Children's House | 15.2 |
Montessori | Pre-KG-5 | 36 | 9.2 | Nonsectarian |
| Montessori Children's Elementary | 15.2 |
Montessori | Pre-KG-5 | 36 | 6.5 | Nonsectarian |
| Ramona Lutheran School | 15.2 |
Regular elementary or secondary | Pre-KG-8 | 102 | 14.6 | Lutheran Church - Missouri Synod |
| Christ Lutheran School | 15.9 |
Regular elementary or secondary | Pre-KG-8 | 197 | 16.0 | Lutheran Church - Missouri Synod |
| Kinder-care Learning Center | 15.9 |
Early childhood program/child care center | Pre-KG-KG | 16 | 8.4 | Nonsectarian |
| Taproot Montessori-la Mesa | 16.0 |
Montessori | Pre-KG-KG | 5 | 5.0 | Nonsectarian |
| St Martin Of Tours Academy | 16.1 |
Regular elementary or secondary | KG-8 | 261 | 23.1 | Roman Catholic |
| St John Of The Cross School | 16.2 |
Regular elementary or secondary | Pre-KG-8 | 512 | 22.3 | Roman Catholic |
| Calvary Chapel La Mesa Christian School | 16.3 |
Regular elementary or secondary | KG-8 | 96 | 15.7 | Christian (no specific denomination) |
| College Center Montessori School | 16.6 |
Montessori | Pre-KG-6 | 32 | 15.2 | Nonsectarian |
| Christian Creative Learning Academy | 16.8 |
Regular elementary or secondary | Pre-KG-5 | 46 | 11.5 | Baptist |
| Green Hills Learning Center | 17.0 |
Special program emphasis | Pre-KG-KG | 15 | 15.0 | Nonsectarian |
| Mt Olive Lutheran Preschool | 17.1 |
Early childhood program/child care center | Pre-KG-Trans. KG | 14 | 10.8 | Lutheran Church - Missouri Synod |
| Eastlake Church Children Center | 17.3 |
Early childhood program/child care center | Pre-KG-KG | 11 | 11.0 | Christian (no specific denomination) |
| Christian Elementary School | 17.3 |
Regular elementary or secondary | Pre-KG-6 | 116 | 13.8 | Baptist |
| St Therese Academy | 17.6 |
Regular elementary or secondary | Pre-KG-8 | 272 | 11.9 | Roman Catholic |
| Learning Adventure School | 17.7 |
Regular elementary or secondary | KG-7 | 30 | 6.1 | Nonsectarian |
| Cornerstone Christian School | 17.9 |
Regular elementary or secondary | KG-8 | 117 | 10.5 | Christian (no specific denomination) |
| Montessori Child Development Center | 18.1 |
Montessori | Pre-KG-KG | 14 | 1.8 | Nonsectarian |
| Childrens Preschool Learning Center | 18.2 |
Early childhood program/child care center | Pre-KG-KG | 12 | 12.0 | Nonsectarian |
| Discovery Isle Child Development Center | 18.3 |
Early childhood program/child care center | Pre-KG-KG | 17 | 17.0 | Nonsectarian |
| Blessed Sacrament Parish School | 18.7 |
Regular elementary or secondary | Pre-KG-8 | 247 | 18.6 | Roman Catholic |
| Bonita Country Day School | 19.0 |
Regular elementary or secondary | Pre-KG-4 | 90 | 8.3 | Nonsectarian |
| Growing Place Montessori Preschool | 19.1 |
Montessori | Pre-KG-1 | 21 | 4.7 | Nonsectarian |
| New Bridge School | 19.2 |
Special education | 1-8 | 55 | 6.1 | Nonsectarian |
| Adventure Days Preschool | 19.2 |
Early childhood program/child care center | Pre-KG-KG | 10 | 10.0 | Baptist |
| The Waldorf School Of San Diego | 19.6 |
Special program emphasis | KG-8 | 256 | 14.8 | Nonsectarian |
| Discovery Isle | 19.7 |
Early childhood program/child care center | KG-KG | 22 | 11.0 | Nonsectarian |
| Chabad Hebrew Academy | 19.8 |
Regular elementary or secondary | Pre-KG-8 | 189 | 5.1 | Jewish |
| Oak Knoll Montessori #2 | 19.9 |
Montessori | Pre-KG-1 | 20 | 5.7 | Nonsectarian |
| Country Montessori School Of Poway | 20.1 |
Montessori | Pre-KG-5 | 95 | 4.3 | Nonsectarian |
| Inst Effective Ed/dba Childrens Workshop | 20.2 |
Special education | Pre-KG-6 | 25 | 3.6 | Nonsectarian |
| Children's Workshop | 20.2 |
Special education | KG-8 | 33 | 6.6 | Nonsectarian |
| Nazareth School | 20.2 |
Regular elementary or secondary | Pre-KG-8 | 270 | 21.6 | Roman Catholic |
| St Michael School | 20.2 |
Regular elementary or secondary | KG-8 | 537 | 17.2 | Roman Catholic |
| St Michael Academy | 20.3 |
Regular elementary or secondary | Pre-KG-8 | 204 | 17.3 | Roman Catholic |
| Our Lady Of The Sacred Heart School | 20.5 |
Regular elementary or secondary | Pre-KG-8 | 152 | 15.8 | Roman Catholic |
| International Preschool & Kindergarten | 20.5 |
Early childhood program/child care center | Pre-KG-KG | 8 | 8.0 | Nonsectarian |
| St Rita's School | 20.5 |
Regular elementary or secondary | Pre-KG-8 | 200 | 19.8 | Roman Catholic |
| Scripps Montessori School | 20.6 |
Montessori | Pre-KG-6 | 40 | 4.8 | Nonsectarian |
| Montessori American School | 20.7 |
Montessori | Pre-KG-KG | 22 | 2.7 | Nonsectarian |
| Incarnation Lutheran Preschool | 20.8 |
Early childhood program/child care center | Pre-KG-KG | 5 | 6.2 | Evangelical Lutheran Church in America |
| Mira Mesa Christian School | 21.0 |
Regular elementary or secondary | KG-6 | 70 | 10.8 | Christian (no specific denomination) |
| Bonita Learning Academy | 21.0 |
Early childhood program/child care center | Pre-KG-KG | 16 | 1.6 | Nonsectarian |
| Mt Erie Christian Academy | 21.2 |
Regular elementary or secondary | KG-6 | 90 | 9.0 | Baptist |
| St Didacus School | 21.2 |
Regular elementary or secondary | Pre-KG-8 | 249 | 20.8 | Roman Catholic |
| St Columba Elementary School | 21.5 |
Regular elementary or secondary | KG-8 | 245 | 21.5 | Roman Catholic |
| Christ The Cornerstone Lutheran Academy | 21.9 |
Regular elementary or secondary | Pre-KG-6 | 93 | 13.1 | Lutheran Church - Missouri Synod |
| Soille San Diego Hebrew Day School | 22.0 |
Special program emphasis | Pre-KG-8 | 217 | 10.8 | Jewish |
| Gretel's Cottage Preschool | 22.1 |
Alternative/other | Pre-KG-1 | 7 | 2.1 | Nonsectarian |
| North Park Christian School | 22.1 |
Early childhood program/child care center | Pre-KG-KG | 5 | 5.0 | Christian (no specific denomination) |
| Montessori Learning Center | 22.1 |
Montessori | Pre-KG-KG | 20 | 12.5 | Nonsectarian |
| St Patrick's School | 22.1 |
Regular elementary or secondary | KG-8 | 174 | 15.1 | Roman Catholic |
| Wee Care Preschool | 22.2 |
Early childhood program/child care center | Pre-KG-KG | 21 | 1.2 | Nonsectarian |
| Faith Community School | 22.2 |
Regular elementary or secondary | KG-6 | 140 | 17.5 | Pentecostal |
| Children's Growing Center | 22.3 |
Early childhood program/child care center | Pre-KG-KG | 12 | 12.0 | Methodist |
| St Jude Academy | 22.4 |
Regular elementary or secondary | Pre-KG-8 | 167 | 12.6 | Roman Catholic |
| Nativity Prep Academy | 22.5 |
Regular elementary or secondary | 6-8 | 62 | 6.9 | Roman Catholic |
| Carmel Mountain Preschool | 22.5 |
Early childhood program/child care center | Pre-KG-KG | 18 | 6.0 | Nonsectarian |
| St John''s Episcopal School | 22.6 |
Regular elementary or secondary | Pre-KG-8 | 408 | 14.4 | Episcopal |
| St Pius X School | 22.6 |
Regular elementary or secondary | KG-8 | 311 | 25.7 | Roman Catholic |
| Good Shepherd Catholic School | 22.7 |
Regular elementary or secondary | KG-8 | 291 | 19.0 | Roman Catholic |
| St Rose Of Lima School | 22.8 |
Regular elementary or secondary | KG-8 | 335 | 24.6 | Roman Catholic |
| Christian Academy Of Chula Vista | 23.0 |
Early childhood program/child care center | Pre-KG-KG | 9 | 9.0 | Baptist |
| Pilgrim Lutheran School | 23.1 |
Regular elementary or secondary | KG-8 | 185 | 18.7 | Lutheran Church - Missouri Synod |
| Islamic School Of San Diego | 23.2 |
Regular elementary or secondary | KG-8 | 152 | 9.1 | Islamic |
| The Children''s Learning Academy Of San Diego Cen | 23.3 |
Special education | KG-8 | 39 | 7.8 | Nonsectarian |
| Our Ladys School | 23.5 |
Regular elementary or secondary | Pre-KG-8 | 210 | 21.0 | Roman Catholic |
| Reformation Lutheran School | 23.6 |
Regular elementary or secondary | Pre-KG-8 | 73 | 12.0 | Wisconsin Evangelical Lutheran Synod |
| Southwestern Christian School | 23.6 |
Regular elementary or secondary | KG-6 | 208 | 13.3 | Church of Christ |
| Chula Vista Christian Elementary School | 23.7 |
Regular elementary or secondary | KG-7 | 70 | 11.5 | Christian (no specific denomination) |
| Holy Family School | 23.8 |
Regular elementary or secondary | Pre-KG-8 | 173 | 15.2 | Roman Catholic |
| Emmaus Today Christian Montessori School | 23.8 |
Montessori | Pre-KG-1 | 10 | 1.4 | Nonsectarian |
| Child's Primary School, The | 24.2 |
Regular elementary or secondary | KG-8 | 93 | 8.8 | Nonsectarian |
| City Tree Christian School | 24.3 |
Regular elementary or secondary | Pre-KG-8 | 178 | 13.4 | Presbyterian |
| St Vincent De Paul Elem School | 24.4 |
Regular elementary or secondary | KG-8 | 223 | 19.2 | Roman Catholic |
| Kinderhouse Montessori School | 24.4 |
Montessori | Pre-KG-KG | 15 | 1.1 | Nonsectarian |
