Abstract Mathematics and sciences are key subjects in the Kenya Secondary school curriculum perennial poor performance and gender disparity in national examinations in these subjects continue to cause concern to educators and the general public. The purpose of this study is to investigate the influence of gender on academic performance of students in public secondary schools in mathematics and sciences. A study will be carried out in Uasin-Gishu West District Rift-Valley Province Kenya. A causal comparative research design will be used to investigate the influence of students gender on academic perfo1mance in mathematics and science, stratified sampling technique will be used to categorize the schools into single random sampling technique will be employed to select schools from each category. Respondents from each of the selected schools will be chosen through simple random sampling tec!rnique. The main instrument of data collection will be the questionnaire. Data obtained will be analyzed using both descriptive and inferential. The findings of this study will equip teacher, policy -makers and other stakeholders with knowledge on how to improve the academic performance in mathematics and sciences as well as achieve gender parity.