This study intended to investigate School based factors affecting girls' performance in mixed secondary schools. The objectives of the study were to determine school-based factors, which affect girls' academic performance (KCSE) in mixed secondary, to suggest the possible strategies to counter the school based factors which affect girls' academic performance. The study sampled mixed Secondary Schools which are twelve in number using simple random technique to select six schools. From the sampled schools, an equal numbers of students were selected from form four classes in each school totaling 160. Sixty (60) teachers were included in the study and six (6) head teachers .Data was collected using questionnaires for students and teachers. Interviews were for head teachers. The research employed a mixed method design technique. Data was analyzed using descriptive statistics i.e. frequencies, percentages, mean and Standard deviation. Scientific Package for Social Sciences (SPSS) was also used. The findings of the study were to provide to the education stakeholders to come up with strategies for countering the school based factors affecting girl's academic performance in KCSE in Nakuru Municipality. From the research findings, it was established that school based factors affecting girls' performance were KCPE intake, time wastage, and boy/girl relationship. The recommendations made were, there should be more guidance and counselling in schools, increase bursaries, inviting resource persons to talk to girls, special relationship between girls and female teachers and separation of girl's classes from boys.