Despite the evident effects of the epidemic on the education sector, there has been no systematic research to look at its impact on education governance in Uganda, in terms of the performance of the descriptive and prescriptive roles of the different actors in the sector. There is still a paucity of data that quantitatively and qualitatively describe and analyse the impact of HIV/AIDS on education sector governance in respect to staff attrition, absenteeism, expenditure, financial planning, human resource planning and management. The overall objective of the study is therefore to go some way to redressing these gaps, by investigating the impact of HIV/AIDS on governance in the education sector with respect to operational effectiveness, budgetary implications, staff morale and productivity and decision-making at Ministry of Education and Sports (MoES) headquarters, semi-autonomous institutions and district level education governance structures. Specifically, the study seeks to: establish the impact of staff illness on the daily activities and governance functions of the sector; establish how staff mortality affects sector governance; examine resources drawn out of the sector due to HIV/AIDS-related illness and death, and examine how the sector sees itself to be coping with absenteeism and attrition among staff.