The Religious Education (RE) programme at St. Margaret College Secondary School Verdala, Cospicua offers students a comprehensive foundation in ethical, historical, and spiritual learning, primarily rooted in the Catholic tradition while fostering respect for a multicultural society. Depending on the educational level, the RE curriculum provides distinct opportunities for students.

In Years 9 through 11, RE is taught as a core subject. It provides students with an understanding of the Bible, the Christian creed, liturgy, sacraments, and Christian morality. The modern syllabus focuses on teaching adolescents to interpret religious symbols, respect diverse worldviews, and engage thoughtfully with major world religions in a diverse society. For students who opt out of Catholic Religious Education lessons (typically from Year 7 onwards), Maltese schools offer Ethics as an alternative to ensure all students receive holistic moral framework training.

On voluntary basis, the school RE teachers work hand in hand with the school Spiritual Director offering students regular confession, Holy Masses and prayer spaces service.