The organizational structure of the Union consists of:

1. The General Conference (GC):
It is the supreme authority of the Union, held once every three years.
2. Board of Trustees (CT):
It consists of 40 members. Its main function is to ensure the implementation of the policies and plans of the Union approved by the General Conference and as such approve the plans, regulations and the general budget and provide the necessary financial resources for their implementation.
3. Secretariat:
The supreme executive authority of the Union is presided over and supervised by the Secretary-General. It consists of 16 members who are Assistant Secretary-General (SGAs) at headquarters and in regional branches as well as the Secretary-General and the Deputy Secretary-General.
4. The Secretary-General (SG):
The chief executive of the union.
5. Headquarters:
There are six Assistant Secretary-General (ASGs), working in close coordination with the Secretary-General as follows:
1. ASG Resources and Development
2. Assistant Secretary General for Coordination and Foreign Affairs.
3. Assistant Secretary General for Research and Publishing.
4. ASG for Media and Public Relations.
5. Assistant Secretary General for the project and planning.
6. Assistant Secretary-General for Administrative and Financial Affairs.
6. Regional Branches:
It has 8 branches worldwide headed by ASGS as follows:

1. Assistant Secretary General of the Arab World (Mauritania).
2. Assistant Secretary-General for Africa (Niger).
3. Assistant Secretary-General for Asia (Pakistan).
4. Assistant Secretary-General for North America and Canada Region. (Canada).
5. Assistant Secretary-General for South America and the Pacific (Trinidad).
6. Assistant Secretary-General for Australia and New Zealand N. (Australia).
7. Assistant Secretary-General for Western Europe (Great Britain).
8. Assistant Secretary-General for Eastern Europe (Albania).
7. Advisory bodies and committees:
The Secretary-General (SG) appoints the membership of these bodies, which must operate under its direct supervision. These bodies help SG in performing union functions, all in a given field.
Membership of the Federation is open to every Muslim women's organization convinced and binding union goals. Today there are 50 organizations from around the world affiliated to be the Union.