SDUHSD includes five comprehensive middle schools for grades seven through eight, and four comprehensive high schools for grades nine through twelve. The district also offers an alternative education high school program at the Sunset High School campus in Encinitas.
Students progress to the high schools from five middle schools in the district as follows:
Students who reside in the residential boundaries of Diegueño and Oak Crest Middle Schools are in the boundaries to attend La Costa Canyon High School
Students who reside in the residential boundaries of Carmel Valley, Earl Warren and Pacific Trails Middle Schools are in the boundaries to attend Torrey Pines High School. (Note: Students who reside in the residential boundaries of the Rancho Santa Fe School District are in the attendance boundaries for Torrey Pines.)
Canyon Crest Academy and San Dieguito Academy high schools are designated as schools of choice for grade 9-12 students who reside within the district and participate in the established high school selection process in February prior to the next school year.