Higher education transformation in the Czech Republic has been aimed at increasing the competitiveness of Czech higher education institutions within the European context, as well as strengthening their role as the main sources of innovation for sustainable development in its economic and social dimensions. This transformation has undergone a turbulent development in last years. The paper elucidates some recent legislative amendments and aims of the Ministry of Education's development plans. We also clarify some research steps that have been undertaken to shed light on the next steps in the transformation. The problem with the reform process is that many systemic undertakings come under pressure from changes in policy cycles, governmental priorities, budgeting, and socio-demographic conditions.