The purpose of this study was to assess the administrative challenges and their impacts on academic performance in public secondary schools in Misungwi District. The study was guided by the following specific objective: to identify the administrative challenges that affect academic performance in public secondary schools in Misungwi District, to find out the impacts of administrative challenges on academic performance in Misungwi District and finally to determine the strategies to be employed to solve the administrative challenges to improve academic performance in Misungwi District. The study adopted convergent parallel design. The study targeted all school heads and all teachers of public secondary schools In Misungwi District. 10 schools out of 24 schools were selected to take part in the study. Purposive sampling was used to select 10 heads of school from the sampled schools while simple random sampling was used to select 90 teachers. Data was collected by distributing the questionnaires to the sampled teachers and interview done to heads of the schools in Misungwi District. The data was analyzed using Statistical Package for Social Sciences (SPSS).the data obtained was analyzed using descriptive statistics including percentages and frequency. Pie charts, graphs and frequency distribution tables were used to present the data. The study found that the major administrative challenges that lead to poor academic performance were: lack of teaching and learning materials, few numbers of teachers, students‟ bad discipline, lack of cooperation from the community, geographical location of the school and political interference. All these lead to poor academic performance to both students and the school. The study recommends that: the government should provide enough fund (capitation) to al public secondary school on time to help the school buy teaching and learning materials like books and build enough infrastructure like classes, laboratories, teachers houses and dormitories for students. The community should show cooperation with the school administration by ensuring security to the school properties, buying their children learning materials like books and uniform for them to attend lessons in school.