The study sought to investigate factors contributing to poor academic performance in public secondary school in Kisauni sub-county in Mombasa county. The study was guided by the following research objectives; To determine the extent to which the size of school contributes to poor students’ academic performance in KCSE in Kisauni sub-county, Mombasa county, to establish the extent to which teaching and learning resources contributes to poor students’ academic performance in KCSE in public secondary schools in Kisauni sub-county, Mombasa county Kenya and to access how the indiscipline of students contributes to poor students’ academic performance in KCSE in public secondary schools in Kisauni sub-county, Mombasa county. The study employed descriptive survey research design. Human capital theory was used developed by Adam Smith in the 18th century and John Stuart Mill in the 19th century which holds that the wellbeing of the society is a function of the knowledge and skills of individuals. The study used a targeted 500 students, 60 teachers and 8 principals in public secondary in Kisauni sub-county in Mombasa county. Simple random sampling was used to select schools, students and principals were purposively selected. The research used questionnaires and interviews as the research instruments. The study used Statistical Package for Social Sciences (SPSS) Version 23. Tables and figures were be used to present the analyzed data. The study established that The number of students in class affects the academic performance. There are no adequate books in the schools which affects students’ performance. Teachers used teaching aids to complement the teaching process to allow better understanding of concepts during their lessons. The study recommends that school heads should ensure their schools have adequate learning materials to allow them have adequate access and utilization of learning materials.