The Ministry of Livestock and Fisheries is headed by the Minister, who provides overall policy direction and strategic leadership for the sector.

Supporting the Minister is the Under-Secretary, who serves as the chief administrative and accounting officer of the Ministry and oversees the coordination of all directorates, programs, and institutional operations.

The Ministry works through a network of technical and administrative directorates that support the implementation of national policies, programs, and development initiatives in livestock and fisheries across South Sudan.