| Century Christian School | 0.7 |
Regular elementary or secondary | Pre-KG-8 | 311 | 20.3 | Christian (no specific denomination) |
| Lodi Sda Elementary School | 1.1 |
Regular elementary or secondary | KG-8 | 202 | 18.4 | Seventh-Day Adventist |
| St Anne School | 2.1 |
Regular elementary or secondary | KG-8 | 249 | 19.4 | Roman Catholic |
| Vineyard Christian Middle School | 2.6 |
Regular elementary or secondary | 6-8 | 84 | 28.0 | Christian (no specific denomination) |
| St Peter Lutheran School | 2.9 |
Regular elementary or secondary | Pre-KG-8 | 171 | 14.4 | Lutheran Church - Missouri Synod |
| Happy Hours Preschool And Kindergarten | 3.1 |
Early childhood program/child care center | Pre-KG-Trans. KG | 23 | 23.0 | Church of God |
| Life Training Academy | 6.1 |
Regular elementary or secondary | KG-8 | 36 | 6.4 | Baptist |
| Carden School Of Stockton | 6.4 |
Regular elementary or secondary | KG-8 | 59 | 6.9 | Nonsectarian |
| Oakbrooke Private School | 7.0 |
Regular elementary or secondary | KG-8 | 30 | 7.5 | Nonsectarian |
| Presentation Elementary School | 7.3 |
Regular elementary or secondary | KG-8 | 293 | 17.9 | Roman Catholic |
| Sierra Christian School | 7.9 |
Regular elementary or secondary | KG-8 | 128 | 11.8 | Church of Christ |
| St Luke Catholic Elementary School | 8.2 |
Regular elementary or secondary | Pre-KG-8 | 231 | 16.6 | Roman Catholic |
| Lakeside Christian School K-8 | 8.2 |
Regular elementary or secondary | KG-8 | 515 | 17.2 | Christian (no specific denomination) |
| First Baptist Christian School | 8.5 |
Regular elementary or secondary | KG-8 | 154 | 14.0 | Baptist |
| Stockton Accelerated Institute | 9.5 |
Regular elementary or secondary | KG-6 | 23 | 7.9 | Pentecostal |
| Rainbow School | 9.6 |
Early childhood program/child care center | Pre-KG-KG | 8 | 10.0 | Nonsectarian |
| Annunciation Elementary School | 9.8 |
Regular elementary or secondary | KG-8 | 289 | 27.5 | Roman Catholic |
| Merryhill Schools At Brookside | 10.1 |
Regular elementary or secondary | KG-8 | 254 | 16.9 | Nonsectarian |
| Montessori Children's House | 10.1 |
Montessori | Pre-KG-6 | 31 | 10.3 | Nonsectarian |
| Galt Christian School | 10.2 |
Regular elementary or secondary | KG-8 | 55 | 9.5 | Christian (no specific denomination) |
| New Hope Christian School | 10.3 |
Early childhood program/child care center | Pre-KG-KG | 5 | 2.5 | Assembly of God |
| Valley Christian School | 10.7 |
Regular elementary or secondary | KG-8 | 36 | 6.7 | Christian (no specific denomination) |
| Galt Adventist Christian School | 10.9 |
Regular elementary or secondary | KG-8 | 28 | 14.0 | Seventh-Day Adventist |
| St George Parish School | 11.8 |
Regular elementary or secondary | KG-8 | 236 | 23.6 | Roman Catholic |
| Stockton Sda School | 12.2 |
Regular elementary or secondary | 2-8 | 14 | 14.0 | Seventh-Day Adventist |
| Stockton Seventh-day Adventist | 12.2 |
Regular elementary or secondary | 2-8 | 14 | 14.0 | Seventh-Day Adventist |
| Plumfield Christian Academy | 20.5 |
Regular elementary or secondary | KG-8 | 102 | 11.6 | Christian (no specific denomination) |
| Always Friends Preschool Childcare | 21.0 |
Early childhood program/child care center | Pre-KG-KG | 7 | 7.8 | Nonsectarian |
| St Anthony School | 21.0 |
Regular elementary or secondary | Pre-KG-8 | 268 | 23.5 | Roman Catholic |
| Manteca Christian School | 21.1 |
Regular elementary or secondary | Pre-KG-8 | 121 | 13.6 | Assembly of God |
| Manteca Adventist Christian School | 21.4 |
Regular elementary or secondary | 1-8 | 15 | 15.0 | Seventh-Day Adventist |
| Montessori Country Academy | 22.0 |
Montessori | Pre-KG-KG | 12 | 1.0 | Nonsectarian |
| Elk Grove Montessori School | 22.2 |
Montessori | Pre-KG-KG | 4 | 4.0 | Nonsectarian |
| St Elizabeth Ann Seton Catholic School | 23.0 |
Regular elementary or secondary | KG-8 | 317 | 30.2 | Roman Catholic |
| Little London Montessori | 23.5 |
Montessori | Pre-KG-KG | 4 | 1.0 | Nonsectarian |
| St Peter's Lutheran School | 24.1 |
Regular elementary or secondary | KG-8 | 205 | 17.7 | Other Lutheran |
