The persistence of gender inequality in education in Africa is due to poverty, cultural beliefs and traditions linked to gender-role expectations. This article presents the findings of a study that evaluated the outcomes of the United States Agency for International Development (USAID)-funded Gender Equity through Education (GEE) programme aimed at increasing the participation of girls in education through scholarship and mentoring activities in South Sudan. Using a convergent mixed-method design and feminist critique of gender difference in education approach as the theoretical framework, the study established that the GEE programme was only partially successful. Though increased enrolment and completion of studies by female students in secondary schools and teacher training institutions was noted, the programme failed to deconstruct the prevailing gendered power relations that subordinate women and may have intuitively strengthened them. The programme sought to bring about changes in the educational milieu through modifications of policies and practices related to education access and retention rather than engage in a process leading to a seismic shift in attitudes towards gender in the society.