The relevant ministries, 13 of them, and the Department of Education in Brčko District are the governing bodies of the education system in BiH. Other participating institutions, primarily pedagogical institutes, which are in fact largely composed of ministries also participate in the management system at these levels (entity and cantonal). Ministries and Pedagogical Institutes supervise the implementation of educational programmes in the institutions at all levels. The Ministry also provides funds for the salaries of the education staff - which is the largest part of the total education budget - for all levels of education, except for the lowest level (preschool education), which is provided partly from the funds of the local government, and partly from the government budget due to the introduction of compulsory attendance age before entry to primary school. At the level of secondary education, institutions of regional governments and educational institutions have the legal authority and responsibility to participate in the appointment of principals and other employees of the institutions. At the level of preschool and primary education, institutions of local self-government and educational institutions have the legal authority and responsibility to participate in the appointment of principals and other employees of the institutions.

Higher education institutions have full institutional autonomy in their work.