In the paper, we examine the response of public entities to change of the funding system. Our goal is to assess whether the responses of the monitored entities are in line with the intentions of government efforts. In other words, whether the instruments used and the method of implemented changes have led to fulfilling the original intentions of the government. In this sense, we have focused on examining several factors: 1) clarity of goals for the representatives of public bodies, 2) harmony and differences in the reactions of selected entities to change of the funding system, 3) comparing the intentions of the government and the resulting state, 4) identification of successes and inconsistency in the resulting state and the original intention, but also other externalities. Our research is based on an analysis of government documents, the implementation of structured interviews with representatives of selected universities and ultimately also on quantitative analysis of the year-on-year outcomes of the monitored universities. The findings and the methodology of “New Public Management” with a focus on the area of performance financing are theoretical basis of the conducted research, which is a key element of changes of the funding of universities in the Czech Republic, put into practice in recent years.