The affairs of the ISA are governed by the Assembly of Councils which is composed of all members of the Council of National Associations and the Research Council.

The Council of National Associations consists of one delegate from each member country. The Research Council is composed of representatives of all Research Committees and sponsors scientific activities of the ISA. The rules of functioning of the Research Committees are detailed in Aims and Requirements for Research Committees.

Every four years at the time of the World Congress, the Assembly of Councils elect the President and Vice-Presidents. Each Council elects 8 members of the Executive Committee. The Executive Committee administers the affairs of the Association between these meetings, while the ISA Secretariat executes the decisions and handles administrative matters. Officers of the Executive Committee serve on at least one of the following sub-committees:

• Research Coordinating Committee
• National Associations Liaison Committee
• Programme Committee
• Publications Committee
• Finance and Membership Committee
• ISA delegates of ISA to other international organizations

The Faculty of Political Sciences and Sociology of the University Complutense in Madrid is the host of the Secretariat. Activities of the ISA are financed about 90% from membership dues and sales of publications and 10% from grants of UNESCO/ISSC.

ISA archives are located at The International Institute of Social History (IISH) in Amsterdam, The Netherlands.