This study sought to examine the influence of classroom management on student’s academic performance in secondary schools in Nyang’hwale District. In order to come up with hard and tangible findings, this study employed mixed research approach and descriptive survey research design. The study was guided by three research objectives: to identify challenges facing teachers when managing their classes, to determine the relationship between classroom management and students’ academic performance and to find out strategies which could be used to overcome the challenges facing teachers in classroom management. Heads of school, teachers and students were involved in this study, where by stratified sampling and simple random sampling were employed to get 40 students and 56 teachers and purposive sampling used to obtain 4 heads of school from 4 selected secondary schools. Data was collected through questionnaires, interviews, document analysis, and observation. Pilot study was done in order to measure the validity and reliability of the instruments for the purpose of revise the questions and removing ambiguity .The collected quantitative data were coded and analyzed by using SPSS version 20 and presented by using descriptive statistics like tables, frequencies and percentages. Qualitative data were analyzed based on themes and its categories. Ethical consideration was observed through granted a written permission from department and research permit from RAS and DED. Also the study ensured the safety of respondents in participation and acknowledged all sources used in the study. The study identified that overcrowded classes, lack of physical facilities, lack of strategies to manage students, sitting arrangements and lack of teaching and learning materials all these are challenges which facing teachers in classroom management also the study revealed that some teachers did not respond their daily duties like creating safe learning environment, maintain proper communication, facilitating availability of teaching and learning materials, guidance and counseling and time management affect academic performance. The study recommended that teachers should have different teaching facilities which will enable to control their classroom management by choosing the best management guide lines, heads of school should visit classrooms to see the teaching process in order to make evaluation also curriculum planners should consider teachers of each subject when their planning to change curriculums for different subjects also government should provide seminars and training to teachers ,building classrooms and providing teaching and learning materials. By doing so it will help to reduce the problem of managing the classroom.