The main purpose of this study was to examine impacts of large class sizes on students’ academic performance in Public secondary schools in Nyamagana District. Large class size refers to a number of pupils/ students which exceed the recommended number of students in a class. According to this study the recommended number of students in a class was 40. Academic performance is the outcome of education; the extent to which a student, teacher or institution has achieved their educational goals through examinations or continuous assessment. The study sought to fulfill three main objectives: to find out the average number of students in each class, to evaluate views experienced by teachers in teaching large classes and to explore the challenges of large class size in the teaching learning process. The study was guided by the systems theory and Vygotsky theory. The study adopted descriptive survey design. Questionnaires were used to gather information from head of schools and students while semi structured interview was used with the teachers. The findings of the study revealed that schools have large classes though most teachers and students prefer small classes. Teachers prefer teaching small classes to enable them help the needy students. Lastly, large classes faced many challenges like poor classroom management, less time to cover task, poor interaction among teachers and students, bad behavior/attitudes among students, difficulty to identify weak students and causes truancy to students. The study recommended that, to improve students’ academic performance in public secondary schools, the government and community should construct more infrastructures such as classrooms and to recruit adequate qualified teachers. Large classes should be split into two or more streams to make them manageable.