The Academy's college preparatory program encourages scholars to develop intellectual ability, make moral decisions, and solidify commitments to Catholic values and attitudes. Students read classic literature, study the history of the world from the viewpoint of Western Christian culture, receive the fullness of the Church's moral teaching without modification or embellishment, and are challenged to think for themselves and to write what they think.

Our students study Latin, the language on which Western civilization is built, the knowledge of which assists them in the mastery of a range of studies from English grammar to literature to science to theology. Our program of study prepares scholars for living in this world and arriving in the next.

Upper scholars pursue a course of study that is specified by the administration and is guided in part by college expectations, in part by diploma requirements, and in part by the academy’s educational philosophy. Courses taken each year typically include Theology, English, Mathematics, History, Science, Latin or Greek, and Music. Other subjects offered in the upper school in order to satisfy graduation requirements include Technology Applications, American Government, Speech, Economics, Athletics, and Health. Elective courses in the upper school include supplementary English and Math. Every upper scholar participates in the Accelerated Reader program.

Advanced Placement and Honors Courses: As part of a rigorous college preparatory curriculum, all upper scholars take multiple AP courses, have the opportunity to take several more, and take numerous honors courses.

A long standing tradition at the academy, as at many other college prep schools, is the requirement that each student complete a summer reading assignment. A description of the assignment and list of approved books are provided each spring as the school year ends for the summer. Both new and returning students, even if enrolling during the summer, are expected to complete the summer reading assignment.

Musical excellence is a hallmark of The Atonement Academy. Every Atonement scholar takes a full credit course in choral music every year. Each student is assigned to one of the academy's ten choirs. Choirs in Grades 3 through 12 take turns singing at the daily school Mass. Every choir performs at least twice yearly, in some cases more frequently. Our most proficient choirs are competitive state-wide. Every student is expected to participate fully in the music program.