The study was to examine the impact of school fees on the academic excellence of pupils in primary schools and the objectives of the study were to examine the effects of school fees on academic excellence in primary schools, to assess the causes of school fees defaulting in primary schools and to propose methods to be used on how to improve on school fees payment in primary schools. The researcher used a cross-sectional survey design. The study population was composed of head teachers, teachers, pupils s and parents of Kyakatara Primary School. A sample size of 80 respondents was chosen to participate in the study, both purposive sampling and random sampling techniques were applied to obtain specific categories of respondents. Data Collection Methods used were Questionnaires and Interviews guides. Both qualitative and quantitative techniques were used. Basing on the findings, the study came up with the effects of school fees defaulting on academic excellence in primary schools that leads to school dropouts of pupils, reduces pupils daily attendance, de-motivates pupils and teachers in school, leads to poor service delivery, affects the supply of school scholastic materials and leads to low concentration of students towards their studies. The study further concluded the causes of school fees defaulting as poverty among families, increase of school fees by school administration, poor performance of the school in final exams, famine among families, lack of relationship between parents and school administrators and political interference. The study also concluded with the methods to be used on how to improve on school fees payment, that pupils should pack their personal requirements like lunch and breakfast, payment of school fees in installments, parents / guardians should acquire school fees loans, the school should obtain donations, the school should provide bursaries to students and increase of relationship between parents and school administration. The following recommendations were suggested from findings like lobbing funds from the Ministry of Education and Sports, establishing teachers, pupils and parent’s relationship, involving parents in the school budget, training head teachers in resource mobilization skills and making more research on the impact of instructional material, educational facilities on socio-economic status of pupils, quality of admission and family background should also be conducted.