Croatian educational system at all levels is centrally governed from the Ministry of Science, Education and sports (MSES) and the related national agencies - Education and Teacher Training Agency, Agency for Vocational Education and Training, Agency for Science and Higher Education, Agency for Mobility and EU Programmes and National Center for External Evaluation of Education.

Ministry and the agencies legaly proscribe and accredit educational programs provided by educational institutions at all levels.

Ministry also administers the salaries of teaching staff - which is the major share of the total budget for education - for all levels of education, except for the lowest level (ECEC) which is provided and administered by the local governments.

At the level of middle schools (upper secondary), regional governments and institutions share the responsibility for appointing the school heads and individual staff members.