| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| Cajon Park Elementary School | K-8 | 10300 Magnolia Avenue
Santee, CA | 92071 | (619) 956-2400 | San Diego | public | Santee Elementary |
| Carlton Hills Elementary School | K-8 | 9353 Pike Road
Santee, CA | 92071 | (619) 258-3400 | San Diego | public | Santee Elementary |
| Carlton Oaks Elementary School | K-8 | 9353 Wethersfield Rd.
Santee, CA | 92071 | (619) 956-4500 | San Diego | public | Santee Elementary |
| Chet F. Harritt Elementary School | K-8 | 8120 Arlette Street
Santee, CA | 92071 | (619) 258-4800 | San Diego | public | Santee Elementary |
| Hill Creek Elementary School | K-8 | 9665 Jeremy Street
Santee, CA | 92071 | (619) 956-5000 | San Diego | public | Santee Elementary |
| Prospect Avenue Elementary School | K-8 | 9303 Prospect Avenue
Santee, CA | 92071 | (619) 956-5200 | San Diego | public | Santee Elementary |
| Rio Seco Elementary School | K-8 | 9545 Cuyamaca Street
Santee, CA | 92071 | (619) 956-5500 | San Diego | public | Santee Elementary |
| Santana High School | 8-12 | 9915 North Magnolia Avenue
Santee, CA | 92071 | (619) 956-0211 | San Diego | public | Grossmont Union High School District |
| Santee Alternative School | K-8 | 10250 El Nopal
Santee, CA | 92071 | (619) 956-2490 | San Diego | public | Santee Elementary |
| Santee Success Program School | 7-8 | 10280 North Magnolia Avenue
Santee, CA | 92071 | (619) 956-2453 | San Diego | public | Santee Elementary |
| Shepherd School | K-12 | 9832 Bend Street
Santee, CA | 92071 | (619) 820-5364 | San Diego | private | |
| Sycamore Canyon Elementary School | K-6 | 10201 Settle Road
Santee, CA | 92071 | (619) 956-5400 | San Diego | public | Santee Elementary |
| West Hills High School | 8-12 | 8756 Mast Boulevard
Santee, CA | 92071 | (619) 956-0400 | San Diego | public | Grossmont Union High School District |
