The study was intended to establish the effect of school security and safety on learners’ academic performance in selected primary schools in Majanji Sub County, Busia District. With intent to find out the factors influencing learners’ academic performance as well as identifying the strategies in place to cater for school security and also determine the effect of school security strategies on learners’ academic performance. Findings showed cases of early pregnancies or early marriages, failure to consider children’s rights and presence of learners with emotional problems. Conclusively, an unsafe school is more likely to result in students who have emotional problems, particularly direct victims of violence or bullying. Consider setting up a hotline to allow victims and witnesses to report occurrences in confidence. Some public schools are increasingly enforcing uniforms for all pupils, just like private institutions. Thus, the study recommends that schools work with the parents together with development partners and government to put up security systems in schools for learners’ safety.