| Name | City | Grade range |
|---|---|---|
| Ezequiel Tafoya Alvarado Academy | Madera | elementary |
| Glacier High School Charter | Oakhurst | high |
| Madera County Independent Academy | Madera | K-12 |
| Minarets Charter High | O'Neals | high |
| Mountain Home Charter (Alternative) | Oakhurst | elementary |
| Pioneer Technical Center | Madera | high |
| Sherman Thomas Charter | Madera | elementary |
| Sherman Thomas Charter High | Madera | high |