IFMSA is guided by its National Member Organizations (NMOs), who are able to take active decisions twice a year, during the General Assemblies of IFMSA. NMOs elect the Team of Officials to lead the work of the Federation throughout the year. This Team is supported by the Supervising Council and appoints international coordinators and assistants.

The Executive Board is responsible for the daily management of the Federation and deals with issues such as fundraising, marketing, external relations, finances, administration, development and support to National Member Organisations.

The Regional Directors assist the Executive Board in their tasks on the regional level. They assist with the development and recruitment of National Member Organization of their region, and promote national inter-cooperation and regional opportunities. They also overview the organization of their Regional Meeting, which takes place once a year in each region.

The Standing Committees Directors are responsible of the development of the Federation core activities in six main health fields: public health, medical education, sexual and reproductive health incl. HIV/AIDS, human rights and peace, professional exchanges and research exchanges. They support medical students activities in these fields throughout the world, organize sessions at IFMSA meetings, and provide capacity building opportunities in their field of work.

The Liaison Officers are the visage of the Federation to external partners and organizations IFMSA has official relationships with. They are active in the fields of the six standing committees, and liaise with other institutions, such as the World Health Organization, UNESCO, students and youth organisations, and research and medical associations.

The Supervising Council is responsible for overseeing the actions and decisions made by the Executive Board and Officials of IFMSA. It is a strategic resource and offers impartial and objective advice when asked. The Supervising Council is also able, upon request, to conduct investigations on issues affecting IFMSA.

IFMSA Team of Officials is also supported by a large team of regional and international assistants, who provide assistance in the standing committees, on the regional level and in various organizational related tasks (webmaster, publications, programs, trainings). They are appointed by the Team of Officials at the very beginning of each term.

The Programs Coordinators are appointed by the Executive Board and work closely in collaboration with the Team of Officials and the National Member Organizations to support the monitoring, assessment and recognition of projects and activities conducted by medical students around the world.

Additionally, IFMSA has a permanent secretariat based in the Academic Medical Center in Amsterdam (the Netherlands), which currently employs one permanent staff. The Federation has also a Board of Recommendation, who provide general guidance and institutional support.