The most important decisions regarding the operation of the University are made by the Governing Board, which consists of ministers leading the Prime Minister's Office, the Ministry of Defence, the Ministry of Interior, and the Ministry of Justice, while the Public Administration Under-Secretary of the Ministry of Foreign Affairs and Trade also takes part empowered with consultation rights.

As far as the daily work of the University is concerned, the main decision-making body is the Senate, which is led by the Rector. The work of the Rector is aided by the Vice-Rectors in the various professional fields.

The Vice-Rector for Academic Affairs coordinates all the educational affairs including the Office of Education, the Central Office of Studies, and the Institute of Disaster Management. The Vice-Rector for International Affairs is responsible for establishing and maintaining the international relations of NUPS via the International Relations Office. The Vice-Rector for Scientific Affairs manages all scientific activities of the University, oversees the Doctoral Schools, the Office of Scientific Affairs, the Central Library of the University, the Institute of National Security and scientific quality assurance processes.

Other important positions are that of the Secretary-General and the Chief Financial Director. The Secretary-General is responsible for the Rector’s Office and the central management of the University. The Office of Finance controls and directs the work of the Financial Office and is responsible for all financial matters regarding the operation of NUPS.

The University has four faculties. The Faculty of Military Sciences and Officer Training educates professional military officers for the Hungarian Defense Forces. The Faculty of Law Enforcement trains students in Criminal Administration, Law Enforcement Administration bachelor programs and in a Law Enforcement master program. The Faculty of Public Governance and International Studies aims at educating professional civil servants for all levels of state administration. and center of the international public service and security policy training. The Faculty of Water Sciences, which is the latest faculty of NUPS was established on the the 1st of February 2017. It deals with the management of water rescources that have vital strategic importance.

Besides the five faculties, there are also several inter-faculty institutes at NUPS. These are the Institute for Research and Development on State and Governance, the Institute of National Security, the Institute of Disaster Management and the Centre for Strategic and Defence Studies.

The Students’ Unions are present on both University and faculty level, where active student members represent the rights and interests of fellow students. The rights of the doctoral students are also represented by the Student Union of Doctoral Students.

A diverse set of student colleges for advanced studies are also to be found at NUPS. These not only organize the scientific efforts of students but serve as social organizations too. Members of these student colleges for advanced studies can participate in research projects, study trips and can later publish their results. In addition to the student colleges, scientific student associations can also be found at each faculty, where students can gain extra knowledge in their specific fields of interest.