The purpose of the Theology program at Marquette University High School is to acquaint students with the Catholic/Christian tradition. While the pastoral programs (retreats, liturgies, Shared Life Project, etc.) are more experiential in nature, theology courses focus on a knowledge of the main elements of Catholic Christian tradition. Theology courses also attempt to help students reflect upon and grow in their religious and moral values and beliefs in light of that tradition.

The first three credits of theology are specified: Theology 1 is Biblical Literature, Theology 2 is composed of Moral Decision Making and Sacraments and the Catholic Church, each a semester course, and Theology 3 is composed of Church History and Christian Discipleship, each a semester course. Seniors must enroll in Theological Seminar on the Church and Contemporary Issues and select one senior elective.