| Name | City | Grade range |
|---|---|---|
| Central Valley Christian School | Atwater | K-12 |
| Gospel Defenders Christian Academy | Merced | None |
| Grace Christian | Le Grand | other |
| Grace Mennonite School | Winton | other |
| Highland Preparatory School | Merced | K-12 |
| Joseph Novack Academy | Merced | K-12 |
| King's Christian School | Atwater | elementary |
| Landmark Christian | Atwater | K-12 |
| Longview Mennonite School | Livingston | other |
| Los Banos Adventist School | Los Banos | elementary |
| Merced Christian | Merced | elementary |
| Our Lady Of Fatima | Los Banos | elementary |
| Our Lady Of Mercy | Merced | elementary |
| Our Lady Of Miracles | Gustine | elementary |
| Quiver For Christ | Merced | None |
| St. Anthony | Atwater | elementary |
| St. Luke's Anglican School | Merced | elementary |
| St. Paul Lutheran | Merced | elementary |
| Stone Ridge Christian High | Merced | high |