The Zanzibar Planning Commission is led by the Executive Secretary, who serves as the accounting officer responsible for coordinating and overseeing all institutional activities. The Executive Secretary ensures that development plans, policies, and programs are properly formulated, implemented, and monitored in line with government priorities.

The Commission consists of six departments headed by Commissioners, each responsible for specific analytical and policy functions. It also includes the Administration and Human Resources Department, managed by the Director and a Coordination Office in Pemba that oversees and harmonizes the Commission's activities on the island.