Gender parity in education is much treasured by many countries around the world, thus its realization is high on the agenda of many governments, Kenya included. Despite the Kenya government’s immense effort to eliminate gender disparity in education, girls in Murang’a South sub-county continue to perform poorer than boys. This study investigated the factors contributing to gender disparity in performance of KCSE examination in public mixed day secondary schools in Murang’a South sub-county. The purpose of the study was to investigate and establish factors that contribute to gender disparity in performance of KCSE examination in public mixed day secondary schools in Murang’a South sub-county. Specifically, the objectives of the study were to establish the school-based factors that contribute to gender disparity in KCSE performance in public mixed day secondary schools in Murang’a South sub-county, to establish the home-based factors that contribute to gender disparity in KCSE performance in public mixed day secondary schools in Murang’a South sub-county, to determine the socio-cultural factors that contribute to gender disparity in KCSE performance in public mixed day secondary schools in Murang’a South sub-county, as well as to establish the interventions schools put in place to address the gender disparity. The study adopted a descriptive survey design and was conducted in Murang’a South sub-county. The target population was the 32 principals of public mixed day secondary schools in the sub-county, the 543 teachers and the 4,200 students. Purposive sampling was done to select the principals as well as the form 3 and 4 classes. Systematic sampling was done to select the boys and girls, according to their admission numbers.