Due to the transition process in Croatia that started about three decades ago, higher education institutions (HEIs) are forced to intensively involve themselves in market competition and become market and entrepreneurial oriented in order to keep up with new trends in higher education. The branding process in HEIs has become one of the major activities in creating value and gaining market position in many countries, including Croatia. The aim of this study is to provide a deeper insight into and understanding of differences in brand market value perceptions of students of public and private HEIs in Croatia. Altogether, 443 students (242 from a public HEI and 201 from a private HEI) responded to a questionnaire based on Aaker’s model of brand equity, from which a t-test and a correlation analysis showed that the public HEI was significantly better only in the dimension of other proprietary brand assets, while in the private HEI all other dimensions of brand market value were evaluated better. However, brand market value itself was significantly higher in the public sector HEI, mainly due to the perception of “value for money” and functional benefits, i.e., employability. The study identified several factors that need to be taken into account when branding private and public HEIs in Croatia.