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The Secretariat is headed by the COMESA Secretary-General (Sindiso Ngwenya) of the Common Market who is appointed by the Authority to serve in such office for a term of five years and is eligible for reappointment for a further term of five years.

The Secretary-General and two Assistant Secretary-Generals direct the divisions of the Secretariat. These are Assistant Secretary-General Administration and Finance who is in charge of two divisions namely, Division of Administration and the Division of Budget and Finance. The Assistant Secretary-General Programmes (Ambassador Kipyego Cheluget) is in charge of the following four Divisions: Trade, Customs and Monetary Affairs Division, Infrastructure Development Division, Investment Promotion and Private Sector Development Division and the Gender and Social Affairs Division. He also supervises several projects and programmes such as Climate Change, ComAid and the Yellow Card.

Almost all of the 19 Member States are currently represented among the 180 staff in the 12 units and divisions of the Secretariat. The work of the Secretariat is ‘programme-driven and division-led’. This means that the programmes are carried out by the divisions and units.

Staff members are appointed to hold various offices, subject to the paramount importance of securing the highest standards of integrity, efficiency and technical competence, to the desirability of maintaining the principle of equal opportunities and an equitable distribution of appointments to such offices among citizens of all the Member States.
The Lusaka headquarters allows persons from Member States to bring their culture, history and values to one place, merging them in an effort to meet one of the organization's main functions which is to promote co-operation among member countries.

Not only will you be exposed to different nationalities at the Secretariat headquarters but working at the COMESA Secretariat can also mean travel to these different countries. It's an opportunity to provide a better understanding of different cultures, religions, and ways of life.