| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| Alvin M. Dunn Elementary School | K-5 | 3697 La Mirada Drive
San Marcos, CA | 92078 | (760) 290-2000 | San Diego | public | San Marcos Unified |
| Applied Scholastics Academy | PK-8 | 134 Woodland Parkway
San Marcos, CA | 92069 | (760) 752-1887 | San Diego | private | |
| Applied Scholastics Academy North County | PK-8 | 800 W. Mission Road
San Marcos, CA | 92069 | (760) 752-3125 | San Diego | private | |
| Bayshore Preparatory Charter School | K-12 | 1175 Linda Vista Drive
San Marcos, CA | 92078 | (760) 471-0847 | San Diego | charter | San Marcos Unified |
| Calvary Christian Academy | K-12 | 256 Smilax Road
San Marcos, CA | 92069 | (760) 727-6353 | San Diego | private | |
| Carpe Diem Academy | 1-12 | 3042 Roadrunner Road
San Marcos, CA | 92069 | (760) 727-4287 | San Diego | private | |
| Christian Liberty Academy | 1-12 | 732 Via Barquero
San Marcos, CA | 92069 | (760) 727-3604 | San Diego | private | |
| Community Christian School | K-8 | 1645 South Rancho Santa Fe Road
San Marcos, CA | 92078 | (760) 744-9237 | San Diego | private | |
| Country School, The | 3-12 | 1145 Linda Vista Drive
San Marcos, CA | 92078 | (760) 744-4870 | San Diego | private | |
| Delphi Academy of San Diego (San Marcos location) | K-3 | 134 Woodland Parkway
San Marcos, CA | 92069 | (760) 752-1887 | San Diego | private | |
| Discovery Elementary School | K-6 | 730 Applewilde Drive
San Marcos, CA | 92078 | (760) 290-2077 | San Diego | public | San Marcos Unified |
| Discovery Isle Child Development Center | K | 1655 South Rancho Santa Fe Road
San Marcos, CA | 92078 | (760) 752-8691 | San Diego | private | |
| Foothills High School | 6-12 | 158 Cassou Road
San Marcos, CA | 92069 | (760) 290-2544 | San Diego | public | San Marcos Unified |
| High Tech High North County School | 9-12 | 1420 San Marcos Boulevard
San Marcos, CA | 92078 | (760) 759-2700 | San Diego | charter | SBC - High Tech High |
| High Tech Middle North County School | 5-8 | 1420 West San Marcos Blvd.
San Marcos, CA | 92078 | (760) 759-2750 | San Diego | charter | |
| Knob Hill Elementary School | K-6 | 1825 Knob Hill Road
San Marcos, CA | 92069 | (760) 290-2080 | San Diego | public | San Marcos Unified |
| Mission Hills High School | 7-12 | 1 Mission Hills Court
San Marcos, CA | 92069 | (760) 290-2700 | San Diego | public | San Marcos Unified |
| North Coastal Consortium Schools | 2-12 | 255 Pico Avenue
San Marcos, CA | 92069 | (760) 761-5110 | San Diego | public | San Diego County Office of Education |
| North Region Court School | 2-12 | 255 Pico Avenue
San Marcos, CA | 92069 | (760) 671-5130 | San Diego | public | San Diego County Office of Education |
| Paloma Elementary School | K-5 | 660 Camino Magnifico
San Marcos, CA | 92069 | (760) 290-2199 | San Diego | public | San Marcos Unified |
| Pivot Charter School - San Diego | n/a | 1030 La Bonita Drive
San Marcos, CA | 92078 | (877) 544-1429 | San Diego | charter | Mountain Empire Unified |
| Richland Elementary School | K-5 | 910 Borden Road
San Marcos, CA | 92069 | (760) 290-2400 | San Diego | public | San Marcos Unified |
| San Elijo Elementary School | K-5 | 1615 Schoolhouse Way
San Marcos, CA | 92078 | (760) 290-2600 | San Diego | public | San Marcos Unified |
| San Elijo Middle School | 6-8 | 1600 Schoolhouse Way
San Marcos, CA | 92078 | (760) 290-2800 | San Diego | public | San Marcos Unified |
| San Marcos Elementary School | K-6 | 1 Tiger Way
San Marcos, CA | 92069 | (760) 290-2430 | San Diego | public | San Marcos Unified |
| San Marcos High School | 7-12 | 1615 San Marcos Boulevard
San Marcos, CA | 92078 | (760) 290-2200 | San Diego | public | San Marcos Unified |
| San Marcos Middle School | 6-8 | 650 West Mission Road
San Marcos, CA | 92069 | (760) 290-2500 | San Diego | public | San Marcos Unified |
| St. Joseph Academy | K-12 | 500 Las Flores Drive
San Marcos, CA | 92078 | (760) 305-8505 | San Diego | private | |
| Twin Oaks Elementary School | K-5 | 1 Cassou Road
San Marcos, CA | 92069 | (760) 290-2588 | San Diego | public | San Marcos Unified |
| Twin Oaks High School | 9-12 | 158 Cassou Road
San Marcos, CA | 92069 | (760) 290-2555 | San Diego | public | San Marcos Unified |
| Valley Christian School | K-8 | 1350 Discovery Street
San Marcos, CA | 90278 | (760) 744-0207 | Los Angeles | private | |
| Woodland Park Middle School | 4-9 | 1270 Rock Springs Road
San Marcos, CA | 92069 | (760) 290-2455 | San Diego | public | San Marcos Unified |
