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Cambodia and Malaysia are two Southeast Asian countries at dissimilar levels of socio-economic development. Their higher education systems are also on different developmental paths with varying motivations driving their respective development and progress, but the governance of higher education across these two systems has one striking similarity. Both systems see neoliberal principles and ideologies as a means to guide the development and governance of higher education, while the States, to varying degrees, still exert significant control and ‘guidance’ over the development and institutional governance. This similarity, albeit at varying degrees, can be seen through examining the issues and challenges concerning the governance of higher education in both countries such as reforms in autonomy and accountability as well as the state-university relationship. Beyond recognising this similarity, we argue the need for considering alternative paths of development for higher education in these countries, particularly alternatives that are more suitable and appropriate for the local needs and contexts in each of the two countries.