The Student Council of Hakoniwa Academy is composed of five members, a president, a vice-president, a treasurer, a secretary, and a general affairs manager. The president is voted into office at the beginning of the academic year by the student body, an event overseen by the Election Management Committee. Afterwards, the president is expected to select the other four members as soon as their term begins. Failure to do so can be seen as reason for impeachment, though this is very rarely done, even if the president does not immediately fill the other council positions. The Student Council overseers the majority of the daily running of the academy, from designating club finds to maintaining the school facilities.
Members of the Student Council all wear the same uniform as the other students of Hakionwa Academy, though their uniforms are black as opposed to the usual white to signify that the Student Council is meant to serve the student body. Each member wears the armband of their position within the council on their left arm.
The Student Council has their own office within the academy, complete with three desks and chairs for the members to work at. The first desk is reserved for the president, with the other two desks placed perpendicularly in front of it. The left desk is for the general affairs manager and the secretary, while the right is for the treasurer and the vice-president. Since Medaka Kurokami's inauguration, the room has slowly been filled with flowers, one for each request completed, to the extent that flowers are now being placed in the hallway just outside the Student Council room as well. The flowers are watered and taken care of by Zenkichi Hitoyoshi.
- President: Zenkichi Hitoyoshi
- Vice President: Youka Naze
- Treasurer: Mukae Emukae
- Secretary: Shori Wanizuka
- General Affairs Manager: Kudaki Torai
Medaka's Student Council
See also: List of Student Council Requests
Since Medaka entered office, a suggestion box has been instituted, which allows students to leave requests for the Student Council to fulfill, anonymously if they so choose. The council will take on any request entered into the box, regardless of whether it applies to a specific individual or the entire academy. It is one of the general affairs manager's duties to maintain the suggestion box, as well as check it daily for new requests.
During the battle to decide which Student Council will take over, the members of Medaka's council don the "Student Council's Battle Attire Red Model" (生徒会戦装束 戦拳戦モデル, Seitokai Ikusa Shouzoku Reddo Moderu) for the duration of the competition. This uniform consists of a different jacket, predominantly colored red and white. For the General Affairs Manager's Battle, the group also wore scarves.
- President: Medaka Kurokami
- Vice President: Misogi Kumagawa
- Treasurer: Mogana Kikaijima
- Secretary: Kouki Akune
- General Affairs Manager: Zenkichi Hitoyoshi
Candidate Student Council
After Najimi Ajimu makes herself known to the Student Council, Medaka organizes an attempt to find successors who will be able to continue to stop Ajimu from succeeding at completing the Flask Plan after Medaka and the current Student Council graduate. However, among the many middle school students who appear upon Medaka's summons, only five remain standing when Misogi Kumagawa brutally and bluntly disheartens them with his words. However, unbeknownst to the Student Council (except for Medaka and Kumagawa), the five are actually detachments of Ajimu and are Normal girls.
- Intern: Suishou Kibougaoka
- Intern: Ima Takarabe
- Intern: Kiki Kikitsu
- Intern: Shori Wanizuka
- Intern: Tsugiha Yojirou
Hinokage's Student Council
The Student Council preceding Medaka's, led by president Kuudou Hinokage. Hinokage acted as Hakoniwa Academy's Student Council president for two years before turning the position over to Medaka. During his tenure, Hinokage served as the sole member of the Student Council, as the other members were all eventually driven away by the overwhelming power of his Abnormality, Unknown Hero.
- President: Kuudou Hinokage
Kumagawa's Student Council
After transferring to Hakoniwa Academy, Kumagawa tries to impeach Medaka due to her failure to select a vice-president. By doing so, he would become the new Student Council president himself, and he could place his own Student Council into power, a group composed completely of Minuses. Though Kumagawa initially appears as the new President and is undoubtedly the group's leader, when the competition to decide which Student Council will take over begins, he participates in the General Affairs Manager's Battle. He claims the position of president means nothing to him, as he is only interested in seeing his own plans come to fruition.