Saint Joseph High School operates under a President/Principal model of school leadership. The school is responsible in three primary ways: as a spiritual center, as an academic institution, and as a small business. Hence, the President and Principal share responsibility for the first, the Principal oversees the second, and the President is responsible for the third.

The President is responsible for the Charism of Fr. Andre' Coindre, the founder of the Brothers of the Sacred Heart, and focuses on the future of the institution. His areas of concern include advancement, finance, alumni, public relations, technology, facilities, and fundraising. The Principal is the spiritual leader of the school, directs the daily operation of the school, and is responsible for the academic, athletic, and extra-curricular programs.

There are two Assistant Principals--one is responsible for Admissions and Transportation, Athletics, and Extracurricular Activities; and the other, the Dean of Studies, is responsible for the academic program, including curriculum development and scheduling.

The Dean of Students is responsible for discipline and attendance. The School Leadership is supported in their work by administrative assistants, including the Directors of Campus Ministry, Instructional Supervision, Technology, Guidance, Student Services, and Athletics. The Assistant Principals, in consultation with the Principal, make the final decision in all matters under their jurisdiction.