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 program for 9th-12th grades at the Sunset Continuation High School campus in Encinitas.
Students progress to the four high schools from five middle schools in the district as follows: Students from Oak Crest and Diegueno Middle Schools are in the boundaries to attend La Costa Canyon High School, and students from Earl Warren, Carmel Valley and Pacific Trails Middle Schools are in the boundaries to attend Torrey Pines High School. (Note that students from the Rancho Santa Fe School District are in the attendance boundaries for Torrey Pines.)
While all students living in the district have the option to enroll at either La Costa Canyon or Torrey Pines High Schools within their attendance areas, they are also eligible to attend San Dieguito High School Academy and Canyon Crest Academy, both of which are designed as schools of choice.