The application of the Lean Management concept is at present one of the major issues raised within the process of reforming higher education institutions (HEI). It is assumed that this concept will be as effective in universities as it is in business organizations, despite the fundamentally different character of the former. Value Stream Mapping is one of the most popular tools used in Lean Management. The purpose of this chapter is to show how the application of the VSM can influence Lean Culture. The results of the research showed that the specifics of the processes and organisational context of HEI require its modification and adjustment, also can result in numerous dilemmas. The most important of them are as follows: defining values, determining which actions and activities make up value stream flows and measuring time and other quantities used in process mapping. VSM changes its nature and not only becomes a tool for organisational and technical change in a university but also strongly influences an organisational culture, as well as staff behaviour and attitudes towards continuous improvement, engagement, openness to change, empowerment.