Gender disparities in education outcome indicators are among the most confounding issues that have challenged education researchers in the Philippines. Data collected during the Millennium Development Goals and the Education for All 2015 monitoring and evaluation activities brought attention to this disparity, leading to the conclusion that boys, in general, were underparticipating and underachieving in basic education. This paper interrogates this conclusion because it has influenced how boys and girls are regarded in the context of education, without adequate explanation for the disparities and, ultimately, there have not been corresponding interventions to address boys’ underachievement in school. It is also time to revisit these disparities as the Department of Education institutionalizes the K to 12 reform which mandates gender sensitivity in classrooms and with the larger push for gender equality in and through education through the Education 2030 Framework for Action of the Sustainable Development Goals.