SUPREME STUDENT GOVERNMENT - The Supreme Student Government handles all the concerns of the high school students of MHSS. It is the main representative of the student body in the institution.

BOOK LOVERS - The Book Lovers promotes reading culture among students. Members hold activities to improve their skill in comprehension and vocabulary.

DROP THE BASS DANCE CREW - Drop the Bass Dance Crew is the newest organization of MHSS for dancers - especially hiphop dancers. It aspires to imbibe in its members self-confidence and good showmanship.

ECO-WARRIORS - The Eco-Warriors is the environmental arm of the Malayan High School of Science. They spearhead projects that pertain to taking care of nature.

MALAYAN GEOGRAPHICAL SOCIETY - The Malayan Geographic Society is the Social Sciences association of the Malayan High School of Science. The club organizes activities related to Geography, History, Politics, and other general Social Sciences that are relevant to the development of the school, country, and the global society.

MASCITECH - The MaSciTech is the Math, Science, and Technology club of the Malayan High School of Science. Members of this organization compete in interschool quizzes and competitions.

MUSIKAMALAYAN - MusikaMalayan is the official choir of the Malayan High School of Science.

PEER COUNSELORS - The Peer Counselors is the official student wing of the Center for Guidance and Counseling. They offer peer help and advice and act as ambassadors of goodwill on campus.

SPORTS ORG - Sports Org is the athletics group of the Malayan High School of Science. It coordinates all sports-related activities of the school.

WHIZZY WORKS - Whizzy Works is the student publication of MHSS. It covers and documents all the important events MHSS is involved in on and off campus.