The Directorate is headed by the Director for Citizenship and Immigration Control and comprises of three major departments each headed by a Commissioner.

1. Immigration control: The Department of Immigration control is responsible for border management and issuance of immigration facilities to foreign nationals seeking to work and reside in Uganda
2. Citizenship and Passports Control: The Department of Citizenship and Passports Control is responsible for verification and processing of Uganda Citizenship as well as the administration of national travel documents
3. Inspection and Legal services: The Department of Inspection and Legal services is responsible for legal advisory services, inspection, investigations, prosecution and removal of undesirable immigrants from Uganda.