| Stockton Baptist School | 2.6 |
Regular elementary or secondary | Pre-KG-10 | 54 | 6.3 | Baptist |
| New World Montessori | 2.6 |
Montessori | Ungraded-Ungraded | 15 | 7.5 | Nonsectarian |
| New Harvest Christian School | 4.0 |
Regular elementary or secondary | Pre-KG-12 | 29 | 4.9 | Christian (no specific denomination) |
| Children's Home Of Stockton Nps | 5.1 |
Special education | 3-12 | 106 | 8.8 | Nonsectarian |
| Samuel N Hancock School | 5.4 |
Regular elementary or secondary | KG-12 | 22 | 5.5 | Pentecostal |
| Apostolic Christian Academy | 7.3 |
Regular elementary or secondary | 2-12 | 26 | 8.7 | Assembly of God |
| North Valley School | 7.6 |
Special education | KG-12 | 73 | 10.4 | Nonsectarian |
| Mokelumne River School | 8.7 |
Regular elementary or secondary | Pre-KG-12 | 215 | 11.9 | Christian (no specific denomination) |
| Central Valley Baptist School | 16.8 |
Regular elementary or secondary | KG-12 | 41 | 5.4 | Baptist |
| South San Joaquin Education Center | 17.4 |
Special education | 6-12 | 19 | 9.5 | Nonsectarian |
| Ripon Christian Schools | 22.0 |
Regular elementary or secondary | KG-12 | 694 | 16.0 | Calvinist |
| Tobinworld Ii | 23.0 |
Special education | KG-12 | 69 | 13.8 | Nonsectarian |
| Modesto Christian School | 24.3 |
Regular elementary or secondary | KG-12 | 653 | 14.0 | Assembly of God |
| Modesto Christian High School | 24.4 |
Regular elementary or secondary | KG-12 | 653 | 10.3 | Assembly of God |
| Gateway Christian School | 24.6 |
Regular elementary or secondary | KG-12 | 171 | 13.6 | Christian (no specific denomination) |
