The neoliberalisation of higher education in post-communist central and eastern Europe, the new EU member states, is not seen as being distinct. Implementation of the Bologna Process and Lisbon Strategy means it has become part of the competitive global sphere of higher education. The transformation of post-communist higher education has attracted little attention, but it is in fact an example of an unprecedented radical 25 year-long transformation: from centralised non-research-orientated communist policy to the radical autonomous Humboldtian environment that emerged after the fall of communism to a strong European neoliberalisation. This article highlights not only the gradual and unique nature of these processes but also shows how they have merged to form the current neoliberalist hybrid. Focusing primarily on former Czecho-Slovakia and the subsequent Slovak and Czech Republics, it details the education policy strategies and initiatives that have contributed to this process. By examining the new educational policy framework at a Slovak university, it shows how Humboldtian culture encountered neoliberal culture: a distinct feature of post-communist neoliberalisation. It is suggested that the Slovak and Czech implementation of neoliberalism has not proved immune to forms of governance similar to those found under communism; rather the two have fused together.