In the last decade, when universal primary education (UPE) was introduced, there has been a tremendous enrolment for the program. However there are concerns on the quality of education given the challenges of enrolment, pupil teachers, ratio and abolition of payment for school lunches among other challenges. The objective of this study is to examine the pupil performance and the extent to which Institutional, community and management challenges are associated with pupil performance. The analysis was carried out using the nationally representative Uganda National Service Delivery survey of 2004.