Following the formation of the Government of the then Southern Sudan in 2005 as provided for in the Comprehensive Peace Agreement (CPA) which was inked between the National Congress Party and the SPLM, which gave Southern Sudan semi-autonomy in rendering basic services including education to its citizens, the Ministry of was established with a number of directorate one of which was the Secretariat of Examinations. The Secretariat became autonomic in 2013 following the formation of its governing Council, the South Sudan National Examinations Council. In the year 2017, the Council of Ministers directed a separation of the Ministry of General Education and the Council for effective management of Examinations and as stipulated in the National Examinations Council Act, 2011
The South Sudan National Examinations Council is the sole examining body in the Republic of South Sudan that is mandated to conduct CPE, CSE and vocational examination in the Country.
The Secretariat is headed by a Secretary General who is the accounting officer and chief executive officer for the Council. The Secretariat is composed of five departments (Administration and Finance, Primary School Exams, Secondary School exams, Research and Evaluation and the Printing Press).
The council is composed of 39 members. Vice chancellors of Public Universities, Directors General in the National Ministry of Education, representative of key government institutions such as Finance, Public Service, Interior and National Security are members of the Council. The membership is drawn as stipulated in the National Examinations Council Act 2011.