The program governance falls under the umbrella of a Memorandum of Understanding between Sudan Federal Ministry of Health (FMoH) and EMPHNET. The program is affiliated to the General Directorate of Health Emergency and Epidemic Control at FMoH. Furthermore, the program has a strategic plan for the years 2019-2023 that encompass the program vision, mission, goals and objectives. The strategy focuses on generating field epidemiologists at all levels (federal, state and locality level) while ensuring high quality training is maintained.

A core governing body in the program is the Technical Advisory Committee, which is headed by the FETP Director and composed of members from the program team, EMPHNET, WHO, Human Resource for Health Directorate and senior Epidemiologists. Additionally, Sudan FETP is a certified member of the Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET) since 2018.