| North County Christian School | Bonsall | 1-12 | 129 | not reported | Christian (nondenominational) |
| Village Gate Children's Academy | Cardiff By the Sea | K-8 | 120 | 9 | Nonsectarian |
| Army & Navy Academy | Carlsbad | 7-12 | 258 | 8.3 | Nonsectarian, all-boys |
| Aspirations School of Learning | Carlsbad | PreK-Transitional K | 43 | 3.4 | Nonsectarian |
| Carlsbad Christian Academy | Carlsbad | PreK-8 | 151 | 15 | Wisconsin Evangelical Lutheran Synod |
| Carlsbad Country Day School | Carlsbad | PreK-K | 24 | not reported | Nonsectarian |
| Casa Montessori de Carlsbad | Carlsbad | PreK-K | 1 | not reported | Nonsectarian |
| La Costa Valley Preschool & Kindergarten | Carlsbad | PreK-Transitional K | 12 | 12 | Nonsectarian |
| Redeemer By the Sea Lutheran Kindergarten&preschl | Carlsbad | PreK-Transitional K | 33 | 16.5 | Lutheran Church (Missouri Synod) |
| St. Patrick Catholic School | Carlsbad | K-8 | 478 | 21.3 | Roman Catholic |
| Village Montessori School | Carlsbad | PreK-Transitional K | 15 | 15 | Nonsectarian |
| Berean Bible Baptist Academy | Chula Vista | PreK-8 | 13 | 2.4 | Baptist |
| Bonita Learning Academy | Chula Vista | PreK-Transitional K | 20 | 10 | Nonsectarian |
| Calvary Christian Academy | Chula Vista | PreK-8 | 358 | 16.3 | Christian (nondenominational) |
| Eastlake Community Church Preschool | Chula Vista | K-Transitional K | 35 | 6.5 | Christian (nondenominational) |
| Green Hill Bilingual Learnind Academy | Chula Vista | K | 5 | 5 | Nonsectarian |
| Kinderland Montessori | Chula Vista | PreK-5 | 38 | 2.2 | Nonsectarian |
| Mater Dei Catholic H.S. | Chula Vista | 9-12 | 1,146 | 16.6 | Roman Catholic |
| Mater Dei Catholic High School | Chula Vista | K-12 | 1,659 | 16 | Roman Catholic |
| Montessori American School | Chula Vista | PreK-Transitional K | 39 | 6.5 | Nonsectarian |
| Montessori Explorer Elementary | Chula Vista | PreK-3 | 19 | 4.9 | Nonsectarian |
| Montessori Hills Academy | Chula Vista | K | 14 | 14 | Nonsectarian |
| South Bay Christian Academy | Chula Vista | K-12 | 35 | 6.4 | Pentecostal |
| St. Pius X School | Chula Vista | PreK-8 | 250 | 14 | Roman Catholic |
| St. Rose of Lima School | Chula Vista | PreK-8 | 315 | 19.7 | Roman Catholic |
| Victory Christian Academy | Chula Vista | K-12 | 316 | 13.6 | Lutheran Church (Missouri Synod) |
| Christ Church Day School | Coronado | K-6 | 92 | 7.3 | Episcopal |
| Leport Montessori | Del Mar | PreK-6 | 45 | 4.5 | Nonsectarian |
| Winston School | Del Mar | 6-12 | 94 | 6.2 | Nonsectarian |
| Christian Elementary School - West Campus | El Cajon | K-6 | 204 | 16.9 | Baptist |
| Christian Elementary School-East Campus | El Cajon | PreK-6 | 476 | 16.1 | Christian (nondenominational) |
| Dayspring Christian Learning Center | El Cajon | PreK-Transitional K | 10 | 10 | Pentecostal |
| El Cajon Seventh-Day Adventist Christian School | El Cajon | K-8 | 24 | 12 | Seventh-Day Adventist |
| Foothills Christian High School | El Cajon | 9-12 | 262 | 11.7 | Christian (nondenominational) |
| Holy Trinity Elementary School | El Cajon | K-8 | 141 | 11.8 | Roman Catholic |
| Our Lady of Grace Elementary School | El Cajon | K-8 | 305 | not reported | Roman Catholic |
| Pepper Valley Learning Center | El Cajon | PreK-Transitional K | 34 | 34 | Nonsectarian |
| St. Kieran Catholic School | El Cajon | PreK-8 | 127 | 13.2 | Roman Catholic |
| Taproot Montessori Preschool & Kindergarten | El Cajon | PreK-K | 1 | not reported | Nonsectarian |
| Central Montessori Schools | Encinitas | K | 141 | 8.1 | Nonsectarian |
| Encinitas Country Day School | Encinitas | K-8 | 289 | 9.4 | Nonsectarian |
| Grauer School the | Encinitas | 7-12 | 160 | 5.1 | Nonsectarian |
| Pacific Academy | Encinitas | K-12 | 113 | 7.5 | Nonsectarian |
| Seeds of Hope Academy | Encinitas | 3-7 | 11 | 5.5 | Nonsectarian |
| The Rhoades School | Encinitas | PreK-8 | 302 | 9.6 | Nonsectarian |
| 10x Academy | Escondido | 6-8 | 30 | 7 | Christian (nondenominational), all-boys |
| Arrow Academy | Escondido | 2-8 | 7 | 3.5 | Christian (nondenominational) |
| Balboa School | Escondido | 7-12 | 10 | 5 | Nonsectarian |
| Escondido Adventist Academy | Escondido | K-12 | 143 | 11 | Seventh-Day Adventist |
| Grace Christian School (Changed the Name 6/15) | Escondido | K-8 | 163 | 18.1 | Lutheran Church (Missouri Synod) |
| Kings Academy | Escondido | 1-11 | 50 | 12.5 | Christian (nondenominational) |
| St. Mary School | Escondido | K-8 | 139 | 12.9 | Roman Catholic |
| Alpha and Omega Academy | Fallbrook | K-12 | 27 | 6.6 | Other religious |
| St. Peter the Apostle Catholic School | Fallbrook | K-8 | 191 | 19.9 | Roman Catholic |
| Zion Christian Preschool Kindergarten | Fallbrook | PreK-K | 23 | 10 | Lutheran Church (Missouri Synod) |
| Taproot Montessori Preschool & Kindergarten | Jamul | PreK-K | 3 | 3 | Nonsectarian |
| All Hallows Academy | La Jolla | K-8 | 184 | 12.2 | Roman Catholic |
| Beth Montessori | La Jolla | PreK-K | 7 | not reported | Jewish |
| Day Prep | La Jolla | K-10 | 39 | 3.5 | Nonsectarian |
| La Jolla Country Day School | La Jolla | PreK-12 | 1,110 | 9.3 | Nonsectarian |
| La Jolla Learning Works | La Jolla | 3-4 | 2 | 2 | Nonsectarian |
| La Jolla Village Montessori School | La Jolla | Ungraded | 27 | 6.8 | Nonsectarian |
| San Diego French American School | La Jolla | PreK-8 | 256 | 7.6 | Nonsectarian |
| Stella Maris Academy | La Jolla | K-8 | 173 | 9.5 | Roman Catholic |
| The Bishop's School | La Jolla | 6-12 | 800 | 6.7 | Episcopal |
| The Childrens School | La Jolla | PreK-8 | 188 | 7.3 | Nonsectarian |
| The Gillispie School | La Jolla | PreK-6 | 198 | 8 | Nonsectarian |
| Christ Lutheran Elementary | La Mesa | K-8 | 213 | 17.8 | Lutheran Church (Missouri Synod) |
| Mt Helix Academy - Tiee | La Mesa | PreK-8 | 186 | 8.1 | Nonsectarian |
| Shepherd of the Hills Lutheran School | La Mesa | K-8 | 49 | 16.3 | Wisconsin Evangelical Lutheran Synod |
| St. Martin of Tours Academy | La Mesa | PreK-8 | 194 | 15.8 | Roman Catholic |
| Taproot Montessori Preschool & Kindergarten | La Mesa | PreK-K | 1 | not reported | Nonsectarian |
| Learning Academy | Lakeside | PreK-4 | 25 | 12.5 | Nonsectarian |
| Brookshire International Academy | Lemon Grove | 9-12 | 1,035 | not reported | Nonsectarian |
| First Presbyterian Church Preschool | Oceanside | PreK-K | 16 | 8.4 | Presbyterian |
| Oceanside Adventist Elementary | Oceanside | K-8 | 96 | 18.1 | Seventh-Day Adventist |
| Teri Learning Academy | Oceanside | Ungraded | 30 | 10 | Nonsectarian |
| Teri, Inc. the Country School | Oceanside | 6-12 | 19 | 4.8 | Nonsectarian |
| West Coast Baptist School | Oceanside | K-12 | 34 | 8.5 | Baptist |
| Country Montessori School of Poway | Poway | PreK-5 | 85 | 4.5 | Nonsectarian |
| Legacy Montessori School | Poway | PreK-4 | 18 | 9 | Christian (nondenominational) |
| Montessori Child Development Center | Poway | PreK-K | 7 | 3.5 | Nonsectarian |
| Skills Learning Center | Poway | PreK-Transitional K | 9 | 2.5 | Nonsectarian |
| St. Michael's School | Poway | PreK-8 | 558 | 17.7 | Roman Catholic |
| Montessori Children's Elementary | Ramona | PreK-6 | 38 | 7 | Nonsectarian |
| Ramona Faith Academy | Ramona | 1-12 | 36 | not reported | Christian (nondenominational) |
| Ramona Lutheran Church and School | Ramona | PreK-7 | 60 | 11.3 | Lutheran Church (Missouri Synod) |
| Diegueno Country School | Rancho Santa Fe | K-6 | 147 | 7.4 | Nonsectarian |
| High Bluff Academy | Rancho Santa Fe | 9-12 | 60 | 6.8 | Nonsectarian |
| Horizon Prep | Rancho Santa Fe | PreK-12 | 308 | 7.6 | Christian (nondenominational) |
| The Nativity School | Rancho Santa Fe | PreK-8 | 178 | 10.1 | Roman Catholic |
| Academy of Our Lady of Peace | San Diego | 9-12 | 730 | 17.6 | Roman Catholic, all-girls |
| Aseltine School | San Diego | 1-12 | 35 | 7 | Nonsectarian |
| Bright Horizon Academy | San Diego | PreK-12 | 322 | 10.7 | Islamic |
| Cal Coast Academy | San Diego | 6-12 | 22 | 4.1 | Nonsectarian |
| Carmel Valley Montessori School | San Diego | PreK-Transitional K | 1 | not reported | Nonsectarian |
| Cathedral Catholic High School | San Diego | 9-12 | 1,669 | 16.9 | Roman Catholic |
| Childrens Creative/Performing Arts Acad San Diego | San Diego | PreK-12 | 186 | 11.4 | Nonsectarian |
| Childrens Workshop | San Diego | 1-8 | 51 | 6.4 | Nonsectarian |
| Christ the Cornerstone Lutheran Academy | San Diego | PreK-5 | 54 | 7.7 | Lutheran Church (Missouri Synod) |
| Coastal Christian Academy | San Diego | PreK-8 | 51 | 7 | Christian (nondenominational) |
| Colema Academy | San Diego | 9-12 | 4 | not reported | Nonsectarian |
| Community School of San Diego | San Diego | 7-8 | 7 | 7 | Nonsectarian |
| Cook Education Center | San Diego | 7-12 | 47 | 4.3 | Nonsectarian |
| Cristo Rey San Diego High School | San Diego | 9-12 | 180 | 10.1 | Roman Catholic |
| Del Mar Pines School | San Diego | K-6 | 155 | 8.3 | Nonsectarian |
| Francis Parker School | San Diego | PreK-12 | 1,276 | 10.8 | Nonsectarian |
| Francis W Parker School | San Diego | PreK-12 | 1,280 | 11.1 | Nonsectarian |
| Fred Finch Youth Center Nonpublic School | San Diego | 8-12 | 16 | 8 | Nonsectarian |
| Fusion Academy - San Diego | San Diego | 6-12 | 30 | 2.2 | Nonsectarian |
| Fusion San Diego Scripps Ranch | San Diego | 6-12 | 31 | 2.8 | Nonsectarian |
| Good Shepherd Catholic School | San Diego | PreK-8 | 229 | 17.1 | Roman Catholic |
| Grace Christian School | San Diego | K-3 | 58 | 11.6 | Christian (nondenominational) |
| Human Factor Leadership Academy | San Diego | PreK-12 | 396 | 26.4 | Christian (nondenominational) |
| Japanese Academy of San Diego | San Diego | K-4 | 27 | 5.4 | Nonsectarian |
| Kinderhouse Montessori School | San Diego | PreK-K | 7 | 2.3 | Nonsectarian |
| Lat Online School | San Diego | 1-12 | 32 | 4.6 | Nonsectarian |
| Le Lycee Francais de San Diego | San Diego | PreK-8 | 149 | 9.7 | Nonsectarian |
| Maranatha Christian Schools | San Diego | PreK-12 | 855 | 12.5 | Christian (nondenominational) |
| Maria Montessori School | San Diego | PreK-8 | 108 | 12.1 | Nonsectarian |
| Mission Bay Montessori Academy | San Diego | PreK-6 | 129 | 3.5 | Nonsectarian |
| Montessori School of San Diego | San Diego | PreK-3 | 25 | 6.2 | Nonsectarian |
| Nativity Prep Academy | San Diego | 6-8 | 70 | 11.7 | Roman Catholic |
| Nazareth School San Diego | San Diego | PreK-8 | 259 | 17.3 | Roman Catholic |
| Notre Dame Academy | San Diego | PreK-8 | 221 | 12.3 | Roman Catholic |
| Ocean View Christian Academy | San Diego | PreK-12 | 432 | 17.9 | Baptist |
| Our Ladys School | San Diego | PreK-8 | 183 | 14.8 | Roman Catholic |
| Pioneer Programs-Community School of San Diego Hig | San Diego | 9-12 | 49 | 16.3 | Nonsectarian |
| Reformation Lutheran School | San Diego | PreK-8 | 67 | 8.6 | Wisconsin Evangelical Lutheran Synod |
| Sam & Rose Stein Education Center | San Diego | Ungraded | 85 | 7.1 | Nonsectarian |
| San Diego Center for Children Academy | San Diego | 1-12 | 77 | 9.2 | Nonsectarian |
| San Diego Jewish Academy | San Diego | PreK-12 | 156 | 12 | Jewish |
| Scripps Montessori School | San Diego | PreK-5 | 41 | 3.4 | Nonsectarian |
| Scy High (Southern California Yeshiva High School) | San Diego | 9-12 | 28 | 3.3 | Jewish, all-boys |
| Soille San Diego Hebrew Bay School | San Diego | PreK-8 | 171 | 7.6 | Jewish |
| St. Augustine High School | San Diego | 9-12 | 729 | 11.4 | Roman Catholic, all-boys |
| St. Charles Borromeo Academy | San Diego | K-8 | 213 | 15.4 | Roman Catholic |
| St. Charles Catholic School | San Diego | K-8 | 182 | 19.4 | Roman Catholic |
| St. Columba School | San Diego | PreK-8 | 211 | 18.5 | Roman Catholic |
| St. Didacus School | San Diego | PreK-8 | 145 | 12.2 | Roman Catholic |
| St. Gregory the Great Catholic School | San Diego | K-8 | 185 | 18.5 | Roman Catholic |
| St. Patrick School | San Diego | PreK-8 | 166 | 13.9 | Roman Catholic |
| St. Paul's Lutheran School | San Diego | K-8 | 150 | 13.2 | Lutheran Church (Missouri Synod) |
| St. Rita's School | San Diego | PreK-8 | 168 | 14.1 | Roman Catholic |
| St. Therese Academy | San Diego | K-8 | 302 | 7.9 | Roman Catholic |
| St. Vincent de Paul Elementary School | San Diego | PreK-8 | 217 | 15 | Roman Catholic |
| Tabernacle Christian Academy | San Diego | PreK-12 | 46 | 5.3 | Pentecostal |
| The Rock Academy | San Diego | PreK-12 | 466 | 10.6 | Christian (nondenominational) |
| The Waldorf School of San Diego | San Diego | PreK-12 | 251 | 8.4 | Nonsectarian |
| Torah High School of San Diego | San Diego | 10-12 | 31 | 2.1 | Jewish, all-girls |
| Urban Skills Center | San Diego | Ungraded | 19 | 6.1 | Nonsectarian |
| Warren-Walker Middle School | San Diego | K-8 | 222 | 14.8 | Nonsectarian |
| Warren-Walker School | San Diego | PreK-5 | 143 | 7.2 | Nonsectarian |
| St. Joseph Academy | San Marcos | K-12 | 355 | 14.8 | Roman Catholic |
| Our Lady of Mt. Carmel | San Ysidro | K-8 | 284 | 22.7 | Roman Catholic |
| Fusion Academy SLB: Solana Beach | Solana Beach | 6-12 | 52 | not reported | Nonsectarian |
| Santa Fe Christian Schools | Solana Beach | K-12 | 1,077 | 12.1 | Christian (nondenominational) |
| Heartland Christian | Spring Valley | PreK-12 | 155 | 10.3 | Christian (nondenominational) |
| Santa Sophia Academy | Spring Valley | K-8 | 218 | 18.2 | Roman Catholic |
| Trinity Christian School | Spring Valley | PreK-8 | 188 | 15.8 | Presbyterian |
| Pamoosa Creek Academy | Valley Center | 2-12 | 7 | 5.4 | Roman Catholic |
| Big Tree Little Preschool Kindergarten | Vista | PreK-K | 9 | 6 | Nonsectarian |
| Building Kidz of Vista | Vista | PreK-K | 1 | not reported | Nonsectarian |
| Kids Town Montessori School | Vista | PreK-3 | 23 | 2.2 | Nonsectarian |
| New Haven Yfs | Vista | 7-12 | 15 | 7.5 | Nonsectarian, all-boys |
| Sanderling Waldorf School | Vista | PreK-6 | 116 | 12.7 | Nonsectarian |
| St. Francis of Assisi Catholic School | Vista | PreK-8 | 199 | 14.6 | Roman Catholic |
| Stars Montessori Academy | Vista | PreK-K | 2 | 2 | Nonsectarian |
| Tri-City Christian School | Vista | PreK-12 | 765 | 14.9 | Christian (nondenominational) |
| Vista Christian School | Vista | K-8 | 210 | 12.4 | Assembly of God |