The General Assembly is the highest administrative authority of the Division. It normally meets every fourth year, on the occasion of an International Congress of History of Science. Between congresses, it is legally represented by the Council or its Executive Committee, which can make provisional decisions, the confirmatory decision resting with the General Assembly.

The Council consists of a President, a First Vice-President, a Second Vice-President, a Secretary General, an Assistant Secretary, a Treasurer, two or more Assessors and the Past President. The Council, or its Executive Committee, is responsible for ensuring the continuity of the Division's policies and the activities in the four-year interval between successive ordinary meetings of the General Assembly. The Council meets at least once every four years, normally on the occasion of an International Congress prior to the General Assembly.

The Executive Committee of the Council consists of the President, the First Vice-President, the Secretary General, and the Treasurer. In the archives, the Executive Committee is sometimes referred to as the "Executive Council" or "Bureau". The Committee meets annually and is charged with the administration of the Division's business and finance and the implementation of resolutions taken by the General Assembly and policies of the Council. During its 1997 meeting in Li├Ęge, the Executive Committee decided that it would set the date of its meetings, whenever possible, each year in the first week of December. In this way, the Committee will be able to examine all the reports and financial requests from the Commissions for the next year in one go.

Historical Commissions are international associations receiving financial assistance from the Division. They are required to report annually to the Secretary General, and to submit reports on their activities to each General Assembly, when the question of their continuation shall be individually put to the vote. Each of the Commissions must conduct its business in accordance with the Statutes and Rules of Procedure of the Division. The Commission Presidents are appointed by the General Assembly upon their Commission's proposal. Each Commission appoints its officers.

Inter-Union Commissions are established on the same basis as Commissions, subject to approval being given by the other ICSU Union concerned.
Since it is formed on the basis of the IAU Commission 41, the Inter-union Commission on Astronomy has a special status. An agreement on this status was signed by the Secretary General of IAU and the Secretary General of IUHPST.

Scientific Sections are administratively autonomous and financially independent bodies. Each is free to levy its own annual subscription, appoint its own officials, formulate its own statutes and apply its own rules of procedure, provided that these do not conflict with those of the Division. In the interest of coordinating the work of the Sections and the Division, each Section may send an Observer to the meetings of the Council.

The Joint Commission is an international association financially dependent upon both the DHST and the DLMPST. Its function is to encourage liaison between historians and philosophers of science, principally through the organisation of joint conferences.