| Brethren Heritage School | 1.4 |
Regular elementary or secondary | KG-12 | 107 | 12.9 | Brethren |
| Modesto Christian High School | 3.4 |
Regular elementary or secondary | KG-12 | 653 | 10.3 | Assembly of God |
| Modesto Christian School | 3.5 |
Regular elementary or secondary | KG-12 | 653 | 14.0 | Assembly of God |
| Mountain View Baptist Academy | 3.5 |
Regular elementary or secondary | 1-11 | 16 | 6.7 | Baptist |
| St Felicissimus School | 3.6 |
Regular elementary or secondary | KG-12 | 12 | 7.5 | Roman Catholic |
| New Harvest Christian | 3.7 |
Regular elementary or secondary | 1-12 | 25 | 4.2 | Christian (no specific denomination) |
| Big Valley Christian | 4.3 |
Regular elementary or secondary | KG-12 | 855 | 8.9 | Christian (no specific denomination) |
| Ripon Christian Schools | 5.2 |
Regular elementary or secondary | KG-12 | 694 | 16.0 | Calvinist |
| St Thomas Aquinas Academy | 6.7 |
Alternative/other | KG-12 | 548 | 94.5 | Roman Catholic |
| Central Valley Christian Academy | 8.4 |
Regular elementary or secondary | Pre-KG-12 | 263 | 15.2 | Seventh-Day Adventist |
| Castillo Christian | 9.0 |
Regular elementary or secondary | KG-12 | 101 | 21.0 | Nonsectarian |
| Riverbank Christian Academy | 9.1 |
Regular elementary or secondary | 1-11 | 6 | 6.0 | Christian (no specific denomination) |
| South San Joaquin Education Center | 9.9 |
Special education | 6-12 | 19 | 9.5 | Nonsectarian |
| Central Valley Baptist School | 11.5 |
Regular elementary or secondary | KG-12 | 41 | 5.4 | Baptist |
| Berean Christian School | 14.4 |
Regular elementary or secondary | 1-12 | 27 | 9.3 | Other Lutheran |
| West Valley Christian School | 14.8 |
Regular elementary or secondary | 1-10 | 16 | 2.3 | Christian (no specific denomination) |
| Reyn Franca School | 16.9 |
Special education | 1-12 | 61 | 10.2 | Nonsectarian |
| Turlock Christian Schools Inc | 17.5 |
Regular elementary or secondary | Pre-KG-12 | 505 | 14.9 | Christian (no specific denomination) |
| Apostolic Christian Academy | 20.9 |
Regular elementary or secondary | 2-12 | 26 | 8.7 | Assembly of God |
| Samuel N Hancock School | 21.9 |
Regular elementary or secondary | KG-12 | 22 | 5.5 | Pentecostal |
| Children's Home Of Stockton Nps | 22.3 |
Special education | 3-12 | 106 | 8.8 | Nonsectarian |
| New Harvest Christian School | 23.2 |
Regular elementary or secondary | Pre-KG-12 | 29 | 4.9 | Christian (no specific denomination) |
| Stockton Baptist School | 25.0 |
Regular elementary or secondary | Pre-KG-10 | 54 | 6.3 | Baptist |
