The study was prompted by the increased concerns by educational stakeholders on the increased challenges facing schools. Specifically, the study sought to establish the management challenges facing school administrators and pupils‟ academic performance in public primary schools. The study was guided by the following objectives; to identify management challenges facing school administrators and pupils‟ academic performance in public primary schools, to find out how management challenges affect pupils‟ academic performance in public primary schools, to determine the possible measures to curb management challenges facing school administrators and pupils‟ academic performance in public primary schools. A sample of ten public primary schools from a population of ninety eight schools was selected for the study. The participants were teachers, school committee chairpersons, ward educational officers, district educational officer, and district school quality assurance. The data gathering was done through the use of questionnaires and interview guide. The findings revealed that there were management challenges facing school administrators and pupils‟ academic performance in public primary school which included insufficient budget, poor cooperation with education stakeholders, over- enrollments of pupils, shortage of infrastructure, lack of teaching/learning resources and shortage of teachers. The identified challenges had negatively affected the schools' and pupils' academic performances because it has lead to pupils‟ absenteeism in schools. To curb these challenges educational stakeholders had to invest more in education by establishing different income generating activities in school. The researcher concludes that educational stakeholders could help in building school infrastructures and finally recommended that, the government should allocate more funds to schools, employ more teachers and school administrators should cooperate with all educational stakeholders in curbing management challenges.