As part of establishing the institutional aspect of the Commission, five departments were set up. The departments are:

 Finance: The department is responsible for effectively and efficiently managing finances of the Commission. It ensures costs are monitored within budgeted levels, accurate and timely financial management and compliance with stated policies and statutory requirements.

Human Resources and Administration:  This division is responsible for provision of human resources services and implementation of strategic human resources programmes. It also provides the Commission with all its outsourced supply through implementation of sound purchasing, transport and stores management strategies.

Research and Programming: This department is responsible for managing and coordinating the various researches and programming operations of the Commission.

Legal and Investigations: The department is responsible for developing guidelines and practices for conduct of effective investigations. It is also responsible for planning and directing the conduct of investigations of possible violations related to gender in accordance with established standards, policies and procedures.

Public Education and Information: The department is responsible for managing the various public education and information operations for the Commission and ensuring efficient information dissemination.

These units are headed by managers who report to two directors: a Director of Programmes heading technical units, and a Director of Finance responsible for support units of Finance, Human Resources and Administration.

The Secretariat is headed by a Chief Executive Officer or Commission Secretary, who is accountable for assisting the Commission through the initiation and implementation of Strategies to promote and protect gender equality.

The approved establishment of the Commission stands at 56 members of staff. However, the Commission has 10 filled positions, representing 18 percent of the required full secretariat.

Of the 10, nine are in the support services department of finance and administration, while at technical level only one legal officer is in place. To enhance the realization of most of its objectives, the Commission approached UN Women for support. UN Women then supported the engagement of a Technical Adviser, whose key mandate was to provide pragmatic support and advice in setting up the Commission. Her role included developing various capacity building initiatives among the Commissioners, institutional capacity building, liaising with various stakeholders on behalf of the Commissioners and facilitating the implementation of the Strategic Plan. To further curb the technical challenges resulting from limited staff, two interns were also engaged.