The AJHS student body is governed by the "Sanggunian ng mga Mag-aaral ng Nakababatang Mataas na Paaralang Ateneo de Manila" (Sanggu-JHS; ). The Sanggu-JHS is led by a chairman, who is aided by a secretary-general and a finance officer, alongside four vice-chairs who supervises each branch of the Sanggu-JHS. These branches are: the Assembly of Class Officers (ACO), which involves the governance of all class officers in each section and batch; the Council of Student Organizations (CSO), which involves the governance of all officers in each student organization referred to as "villages"; and the Athletics Council (AthC), which involves the governance of all varsity team officers.