Education is without a doubt, the sector that holds the key to transformational national development and our ability to compete in the global marketplace and it is singularly the sector that has experienced the worst type of decline in relation to standards, quality and value in Africa. However, the 1990 World Conference on Education for All launched in Jomtien, Thailand has rightly called attention to improving education through better management and expanded access to primary education systems with little attention to secondary education. Therefore, Government of Uganda through the Ministry of Education and Sports (MOES) with support from development partners introduced Universal Education in both primary and secondary schools throughout the country since 1997 and 2006 respectively. The intention was to remove barriers in education, provides flexible and responsive supports, and facilitates lifelong learning for all. Despite the fact that, the government continues to encourage families to send all their school going age children to Universal Secondary Education (USE) schools; the programme has not received the attention it deserves from either the public or the private sector in Uganda. Therefore, this theoretical paper seek to fill the existing long documented unequal academic achievement outcomes among children of different races, ethnic groups and social economic background in all regions of the country. This paper is organized in the following manner; Part I begins with a background and education systems of Uganda, while Part II discusses the major challenges the government is facing in enhancing access, quality and affordable education. Finally, Part III covers practical policy implications and Part IV gives concluding remarks with identified gaps for research.