There are nine academic faculties at St Margaret's.

Arts and Design: Drama; Music; Visual Art; Food and Textiles Technology; Home Economics

Business and Pathways: Learning Enhancement; Junior Business; Senior Accounting; Vocational Education Program 

eLearning and Research Services

English: English; English Extension; English for ESL Learners

Global Studies: Languages - French, German, Mandarin; Legal Studies; Economics

Health and Physical Education

Mathematics: Junior Mathematics; Mathematics A, B and C

Science and Technology: Junior Science; Multi Media; STEM; Science Extension; Biology; Chemistry; Physics; IPT 

Sociocultural Studies: Junior Humanities; Junior History; Junior Geography; Ancient History; Modern History; Senior Geography; Religious and Values Education