Abstract: The paper examines the main challenges facing universities in Bulgaria. It presents organisational issues of risk management in the higher education system and focuses on practices that need to be changed in order to implement risk management. Based on comparative content analysis, it identifies key areas that should be the subject of intervention in educational and scientific organisations in order to achieve efficiency, effectiveness and appropriateness of the process. The paper proposes solutions to improve risk management in the sector. It outlines guidelines for introducing a systematic approach to risk management in order to improve the organisational environment and operational management.