The main decision-making body of IAPSS is the General Assembly (GA). The GA convenes annually and decides on issues of relevance for the existence of the Association and on the long- and medium-term goals of IAPSS. The GA elects all other bodies of the Association: The Executive Committee (ExCom), the Supervisory Committee (SupCom), the Disciplinary Commission, the POLITIKON-IAPSS Journal of Political Science Editorial Board, and the Premium Association Member.

The internal control system is composed of the SupCom and the Disciplinary Commission. The SupCom is the body which supervises the activity of the Association in-between two meetings of the GA. It supervises the work of all other bodies of the Association and reports to the GA. The Disciplinary Commission deals with matters connected to the way the statute is being observed. It decides on sanctions when the statute is not respected.

The POLITIKON-IAPSS Political Science Journal Editorial Board coordinates the issuance of the IAPSS Journal. The Editorial Board coordinates its executive work with the ExCom and maintains sole authority on issues related to the content of the Journal.

The ExCom is the body which has the decisional power in between two meetings of the GA. It manages the Association and implements the decisions of the GA. The ExCom, just as all other elected bodies of IAPSS has a one-year mandate. The members of the ExCom are, in principle, residing in Ljubljana, Slovenia, where the Permanent Seat of the IAPSS is located. The ExCom is in charge of the daily work within IAPSS; therefore it coordinates the executive part of IAPSS.

The Premium Association Member is the local association elected for one year to organize the Annual Conference and the General Assembly of IAPSS.

The ExCom as mentioned above coordinates the executive structure of IAPSS. The executive structure consists of departments. The IAPSS departments are created to ensure the existence of IAPSS and to support the implementation of the IAPSS Strategic Plan as well as of any other activity IAPSS may develop or be part of.

IAPSS' activity is being carried out by implementing projects. The GA Resolutions and the IAPSS Strategic Plan, which is also being adopted by the GA, guides the work of the ExCom in this respect. Projects are the basic activities IAPSS develops for its members and for political science students at large.