The complicated colonial history of the Philippines impacts notions of gender in the Islands. Specifically, institutions with strong foreign roots, such as universities, maintain and challenge gender relations. The Philippines sees multiple gender issues in universities despite government-mandated gender mainstreaming policies for education (CMO-1), yet the influence of colonial values remains overlooked. This article contributes to philosophising Philippine education by providing the history of the country's universities and their role in shaping gender relations. A threefold model of gender structures, relations of power, production and cathexis (emotional attachment), frames historical literature during the Philippines' Spanish and American colonial periods and contextualises the country's gender order. The interplay of religion and higher education during the Philippines' Spanish colonial period reveals why sexuality remains policed by education institutions. The gendering of courses during the American Colonial period details the feminisation of certain disciplines and occupations. Harmful manhood practices adopted during this period continue to affect men in university systems through Philippine fraternities. Lastly, private education perpetuates and maintains power among the elite. The evolution of the Philippine university provides points for analysis for gender issues. These become building blocks to the discourse surrounding the Filipino philosophy of education, by understanding facets of Filipino identity construction, and proposing avenues to explore when decolonising the university.