The Presidium is the foremost elected, political body of IFM-SEI. Headed by the President, the Presidium takes charge of overseeing the development and execution of the strategic work plan, pinpointing educational and political priorities, and supervising the finances of IFM-SEI. The structure of the Presidium includes the President, Vice President, and one representative from each region. Within the regional representation, there must be at least one non-man and one person under 30. Additionally, the Secretary General is a part of the Presidium.

The Control Commission consists of three people and is responsible for the financial control of the organisation – including checking the books and finances of IFM-SEI – and ensuring compliance with the IFM-SEI Constitution and Rules of Procedure.

The secretariat is the operational heart of IFM-SEI and is based in Brussels. The secretariat usually consists of the Secretary General, the Projects manager, the Finance and Office Manager and one or two long-term volunteers. Additional staff members, such as a Project Officers, interns or other volunteers may also make up the secretariat. The Secretary General is responsible for the political and organisations developments in IFM-SEI as well as being responsible for the daily work and coordination of the office, strategic work plan and working groups.