The relationship of academic organizations, especially universities, with the state and the markets, is the basis for the governance of national systems of higher education. In turn, organization's governments respond to the governance arrangements at the national system level, and to the traditions and cultural evolution of each institution. Critical for this relationship is the political economy of national higher education systems; that is, the way higher education is provided and institutions are financed. Considering this scenario, the present article has as its main objective to reflect on some key issues related to the evolution and functioning of the political economy and governance arrangements of national higher education systems in Latin America. For this purpose, selected topics are discussed in the form of an essay and the pertinent academic literature is revised.