| Stockton Baptist School | 0.0 |
Regular elementary or secondary | Pre-KG-10 | 54 | 6.3 | Baptist |
| New Harvest Christian School | 2.2 |
Regular elementary or secondary | Pre-KG-12 | 29 | 4.9 | Christian (no specific denomination) |
| Stockton Christian School | 2.6 |
Regular elementary or secondary | KG-12 | 271 | 19.4 | Christian (no specific denomination) |
| Children's Home Of Stockton Nps | 3.6 |
Special education | 3-12 | 106 | 8.8 | Nonsectarian |
| Samuel N Hancock School | 3.8 |
Regular elementary or secondary | KG-12 | 22 | 5.5 | Pentecostal |
| New World Montessori | 4.9 |
Montessori | Ungraded-Ungraded | 15 | 7.5 | Nonsectarian |
| Apostolic Christian Academy | 6.2 |
Regular elementary or secondary | 2-12 | 26 | 8.7 | Assembly of God |
| North Valley School | 7.2 |
Special education | KG-12 | 73 | 10.4 | Nonsectarian |
| Mokelumne River School | 10.1 |
Regular elementary or secondary | Pre-KG-12 | 215 | 11.9 | Christian (no specific denomination) |
| Central Valley Baptist School | 15.0 |
Regular elementary or secondary | KG-12 | 41 | 5.4 | Baptist |
| South San Joaquin Education Center | 15.3 |
Special education | 6-12 | 19 | 9.5 | Nonsectarian |
| Ripon Christian Schools | 19.8 |
Regular elementary or secondary | KG-12 | 694 | 16.0 | Calvinist |
| Modesto Christian School | 21.9 |
Regular elementary or secondary | KG-12 | 653 | 14.0 | Assembly of God |
| Modesto Christian High School | 22.1 |
Regular elementary or secondary | KG-12 | 653 | 10.3 | Assembly of God |
| St Felicissimus School | 24.1 |
Regular elementary or secondary | KG-12 | 12 | 7.5 | Roman Catholic |
| Brethren Heritage School | 24.4 |
Regular elementary or secondary | KG-12 | 107 | 12.9 | Brethren |
| Tobinworld Ii | 24.6 |
Special education | KG-12 | 69 | 13.8 | Nonsectarian |
| Wood Colony Brethren School | 25.0 |
Regular elementary or secondary | KG-12 | 100 | 9.0 | Other |
