The purpose of this study was to determine the effects of school conflict on student academic performance. School conflicts is a phenomenon that has been witnessed in most secondary schools in Kenya, school conflicts disrupt school programs and lowers performance of the school. School conflicts occurs in different forms such as strikes, riots, unrests among others. The objectives of the study were to determine the causes of school conflict, find out the types of school conflicts and to establish the strategies on school conflicts on student academic performance in Kenyenya sub-county. The study adopted descriptive survey research design using both quantitative and qualitative method. Also, purposive sampling and simple random sampling technique was used to collect data. The target population in this study consisted of 50 public secondary schools, 50 deputy principals teachers and 500 student council leaders in public secondary schools in Kenyenya sub county. Data collection instruments used interview schedule for deputy principals and questionnaires for student council leaders. The researcher collected and analyzed data using a statistical package for social science system. The findings were school conflicts are prevalence among secondary schools, the most type of conflicts was student- teacher conflicts. It was also revealed that conflicts affect academic performance of the learners mainly when learning resources such as desks and books are damaged. Another finding was that conflicts affect student-teacher relations and working relationship between teachers and students are not restored easily after conflicts although most deputy principals and student council leaders are also trained to manage conflicts. The study concluded that conflicts are inventible in schools and it is therefore important that they are managed well. The researcher recommended that safe storage of essential learning materials be enhanced that teachers should be trained on conflict management of public secondary schools. The researcher was hopeful that the findings of the study would be of great benefit to the educational officers, deputy principals, students and parent on the school performance.