Ultimate responsibility for the Graduate School lies with the Board of the Joint Faculties of Humanities and Theology at Lund University. The Board for Third-Cycle Studies of the Joint Faculties of Humanities and Theology is responsible for implementing Board decisions. The Graduate School comes under the remit of the History subject in the Department of History in Lund. The Department appoints a Director of Operations for the Graduate School who, together with the Director of Second and Third Cycle Studies in History, is responsible for the functioning of operations. The Director of Operations and the Director of Studies are assisted by a Deputy Director of Studies, education coordinators and other staff associated with a management group tasked with running the administration.

The Director of Operations for the Graduate School has lead responsibility for the graduate education partnership and for networking. A Collaboration Council acts in an advisory capacity. Its members include representatives of the History subject at the partner universities and of the doctoral students collectively. In turn these subject representatives are responsible for contacts with other subjects with a historical perspective participating in the graduate education partnership.

Up until 2019 the Graduate School financed doctoral student positions at Lund University and partner universities. As from 2019 the Graduate School only finances new doctoral students at Lund University. For doctoral students at other institutions, who are still financed by the Graduate School, the old agreement of 2016 remains in force. Doctoral students are accepted by and employed at one of the collaborating universities. Doctoral students are accepted in accordance with the general provisions of the Higher Education Ordinance and the local regulations of the specific university, and are employed by the specific university. The working language of the Graduate School is Swedish, and most subjects included in the Graduate School require a prospective doctoral student to be able to comprehend texts in Swedish.

The option of joining the network and participating in activities arranged by the Graduate School is also open to doctoral students in Lund who are financed by their faculties or by projects, if they belong to departments that also have doctoral students financed by the Graduate School. The other participating universities offer doctoral students in History, and in subjects where the Graduate School finances doctoral students, the option of taking part in the activities of the Graduate School.