| Name | Address | Enrollment | Grade span |
|---|---|---|---|
| Alvin M. Dunn Elementary School | 3697 La Mirada Drive | 364 | K-5 |
| Bayshore Prep Charter School | 100 North Rancho Santa Fe Road, Suite 110 | 107 | K-12 |
| Discovery Elementary School | 730 Applewilde Drive | 565 | K-5 |
| Foothills High School | 158 Cassou Road | 22 | 9-12 |
| High Tech High North County School | 1420 San Marcos Boulevard | 255 | 9-12 |
| High Tech Middle North County School | 1420 West San Marcos Boulevard | 322 | 6-8 |
| Knob Hill Elementary School | 1825 Knob Hill Road | 550 | K-5 |
| Mission Hills High School | 1 Mission Hills Court | 1,774 | 9-12 |
| North Region Community School | 255 Pico Avenue | 53 | 7-12 |
| North Region Court School | 255 Pico Avenue | 10 | K-12 |
| Paloma Elementary School | 660 Camino Magnifico | 600 | K-5 |
| Richland Elementary School | 910 Borden Road | 551 | K-5 |
| San Elijo Elementary School | 1615 Schoolhouse Way | 513 | K-5 |
| San Elijo Middle School | 1600 Schoolhouse Way | 1,263 | 6-8 |
| San Marcos Adult School | 158 Cassou Road | - | - |
| San Marcos Elementary School | 300 West San Marcos Boulevard | 342 | K-5 |
| San Marcos High School | 1615 San Marcos Boulevard | 1,462 | 9-12 |
| San Marcos Middle School | 650 West Mission Road | 1,150 | 6-8 |
| Twin Oaks Elementary School | 1 Cassou Road | 537 | K-5 |
| Twin Oaks High School | 158 Cassou Road | 67 | 9-12 |
| Woodland Park Middle School | 1270 Rock Springs Road | 1,337 | 6-8 |
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