In the secondary program the classes for students in grades 9 to 12 are departmentalized.  Some secondary students are scheduled into courses that stress more traditional academics; others are scheduled into courses that emphasize applied academics.

Each secondary teacher is assigned one homeroom and acts as the case manager for those students.  Students receive progress grades every nine weeks; final grades are issued at the end of each semester. These report cards differ from the IEP progress reports in that they reflect progress in the curriculum across completion of classroom and homework assignments, class participation, projects, quizzes, and tests. Grades are based on performance within the modified curriculum.

A cumulative transcript documenting all credits earned toward a high school diploma is kept for all students ninth grade and above. Students earn a certificate of completion upon finishing the necessary course work or a high school diploma for completion of coursework AND passing the required exit exams or proficiency tests.  The FrostigSchool is accredited by the Western Association of Schools and Colleges (WASC); all completed courses, earned credits and high school diplomas are also recognized as valid by the California Department of Education.