| Central Valley Baptist School | 3.1 |
Regular elementary or secondary | KG-12 | 41 | 5.4 | Baptist |
| Ripon Christian Schools | 4.7 |
Regular elementary or secondary | KG-12 | 694 | 16.0 | Calvinist |
| Modesto Christian School | 7.4 |
Regular elementary or secondary | KG-12 | 653 | 14.0 | Assembly of God |
| Modesto Christian High School | 7.5 |
Regular elementary or secondary | KG-12 | 653 | 10.3 | Assembly of God |
| Brethren Heritage School | 9.5 |
Regular elementary or secondary | KG-12 | 107 | 12.9 | Brethren |
| Wood Colony Brethren School | 9.9 |
Regular elementary or secondary | KG-12 | 100 | 9.0 | Other |
| St Felicissimus School | 9.9 |
Regular elementary or secondary | KG-12 | 12 | 7.5 | Roman Catholic |
| Apostolic Christian Academy | 11.0 |
Regular elementary or secondary | 2-12 | 26 | 8.7 | Assembly of God |
| Big Valley Christian | 11.4 |
Regular elementary or secondary | KG-12 | 855 | 8.9 | Christian (no specific denomination) |
| Samuel N Hancock School | 12.0 |
Regular elementary or secondary | KG-12 | 22 | 5.5 | Pentecostal |
| Children's Home Of Stockton Nps | 12.4 |
Special education | 3-12 | 106 | 8.8 | Nonsectarian |
| Mountain View Baptist Academy | 12.4 |
Regular elementary or secondary | 1-11 | 16 | 6.7 | Baptist |
| New Harvest Christian | 13.0 |
Regular elementary or secondary | 1-12 | 25 | 4.2 | Christian (no specific denomination) |
| New Harvest Christian School | 13.4 |
Regular elementary or secondary | Pre-KG-12 | 29 | 4.9 | Christian (no specific denomination) |
| Riverbank Christian Academy | 13.8 |
Regular elementary or secondary | 1-11 | 6 | 6.0 | Christian (no specific denomination) |
| St Thomas Aquinas Academy | 14.4 |
Alternative/other | KG-12 | 548 | 94.5 | Roman Catholic |
| Stockton Baptist School | 15.3 |
Regular elementary or secondary | Pre-KG-10 | 54 | 6.3 | Baptist |
| Stockton Christian School | 17.4 |
Regular elementary or secondary | KG-12 | 271 | 19.4 | Christian (no specific denomination) |
| Castillo Christian | 17.4 |
Regular elementary or secondary | KG-12 | 101 | 21.0 | Nonsectarian |
| Central Valley Christian Academy | 17.9 |
Regular elementary or secondary | Pre-KG-12 | 263 | 15.2 | Seventh-Day Adventist |
| New World Montessori | 18.5 |
Montessori | Ungraded-Ungraded | 15 | 7.5 | Nonsectarian |
| North Valley School | 20.5 |
Special education | KG-12 | 73 | 10.4 | Nonsectarian |
| Berean Christian School | 22.8 |
Regular elementary or secondary | 1-12 | 27 | 9.3 | Other Lutheran |
| West Valley Christian School | 23.2 |
Regular elementary or secondary | 1-10 | 16 | 2.3 | Christian (no specific denomination) |
