The past 20 years have been a period of reforms for school systems in Visegrad countries. However, the successful implementation of educational reforms requires effective leaders and managers and, to produce effective leaders, changes in the system of leadership and management programmes need to be adopted. From 2004, the Czech Republic saw a growth of school project activities, with educational projects becoming important tools for supporting innovations in teaching and learning processes. Despite the new system of leadership development, there was a gap between level of headteachers’ competencies and the competency required to manage educational projects successfully. This study focuses on the leadership competencies of project management, particularly risk management, in the context of educational organizations. The survey data were collected through interviews with headteachers, senior teachers and project managers in 118 educational subjects from nine regions of the Czech Republic. The research team acquired data from 300 educational projects. The key findings show that headteachers have difficulty in managing the risks of educational projects. Survey results also indicate that a very high level of risk occurred in 8% of the examined projects, and medium risk, in 27%. It is suggested that training and knowledge-transfer programmes about project management, including risk management, should become priorities when preparing headteachers for their role.