The General Assembly is the supreme and ultimate authority of the World Union of Jewish Students. It convenes in person at least once a year at the Annual WUJS Leadership Congress. The members of the General Assembly consist of one representative from the each of the Member Unions, their votes allocated in conjunction with the Jewish populations of the countries concerned. The General Assembly sets the policy of the Union, and elects the President, Treasurer, and Board.

The WUJS President is elected biennially at the WUJS Congress by the Member Unions to be the leader and voice of the Global Jewish Student Movement. In this position, among other responsibilities, the President maintains contact with all the WUJS Member unions around the world, advocates on behalf of the Jewish students before international authorities, represents the Union at all relevant international functions and organizations. The President leads the Union politically and enacts the policies decided upon by the General Assembly, oversees all Union projects, plans and programming, manages the budget, and maintains relationships with partner organizations and donors.

The members of the WUJS Board consist of (up to) 11 Member Union leaders, elected by the WUJS General Assembly once a year. Their function is to represent the Member Unions to the WUJS President between General Assemblies. They weigh in on matters of policy, content and programming of the Union, and ensure that the objectives of the Union are implemented by the President.