InterGender is managed by a board consisting of representatives from each of the participating partner institutions, and four representatives for the PhD students. The Board members are appointed for three years, while the student members are appointed for one year on a rotating basis. This is to ensure that PhD students from all partner institutions within a three year period will have had representation in the Board.

The Board meets twice a year. It selects an executive Board of five members which together with the Director and the Academic Coordinator is scientifically and economically responsible for the coordination and for carrying out the joint programme of activities. The Director is scientifically and economically responsible for day-to-day management, and is assisted in this task by an Academic Coordinator, on 50% employment. To ensure a high level of communication, the executive board meets at least three times per term and communicates in-between meetings.

The responsibility for the development, coordination and teaching of courses and other activities is delegated from the board of InterGender, to cross-disciplinary and cross-institutional taskforces. These work closely together with local hosts, on the one hand, and with the lead team, consisting of Executive Board, Academic Coordinator and Director, on the other hand.