This is a theoretical paper with a charge to examine the scope and character of gender equality in the education systems of Uganda, Rwanda and South Sudan through a review of cross-national literature using feminist lens to interpret their connotations. While Uganda and South Sudan have invariably sought to enact affirmative action geared at achieving increased access for girl children, Rwanda has by and large focused on shifting from affirmative action to more holistic genderresponsive strategies in its crusade. This, perhaps, is the most convincing notion of salience among the three East African countries; confirming that formal opportunities for equal treatment of girl children ensure neither a shared starting point nor equal outcomes because of different cross-national milieus of change. In Uganda, the flagship of government initiative is the 1997 UPE which has since its launch spurred a big rise in the number of school girls across the country. The extension of the free education policy to 12 years represents Rwanda‟s best bid to attain gender equality; while the Go to School Initiative is South Sudan‟s rarest case of success in promoting access and participation but remains largely embryonic and sporadic. Cultural thinking, economic insecurity and social disadvantage immensely affect the way poor and rural households decide about investing in their girl children‟s education. There is need, therefore, to emphasize the intrinsic developmental value of education over and above the compulsion for productivity and employability. It is audaciously mistaken to establish that gender inequality could be altered by education or within the education system without restructuring sexual division of labour in the home and the market at large. To achieve gender equality in their education systems, Uganda, Rwanda and South Sudan must decode the cultural capital of their social classes and use that knowledge to empower women and girl children at the family and community levels while schools offer prospect. If these initiatives could be further institutionalised, resourced, and embedded in durable policy visions, it is possible for schools to become standard for broader societal transformation.