The study investigates teachers’ method of teaching and academic performance of students in Uganda Certificate of Education in Kisoro district. The objective is to establish the relationship between method of teaching by teachers and academic performance of students in Kisoro district, Uganda. The study adopted a descriptive survey design. One hundred and twenty (120) respondents (teachers) were drawn from one hundred and thirty (130) teachers using stratified sampling technique; and all the four (4) head teachers were selected using census. Questionnaire and interview guide were used to collect data for the study. The content validity index of 0.83 was determined while a reliability of the instrument (questionnaire) was established with the use of pilot study and the valued at 0.72 was obtained. There is a statistically moderate positive and significant relationship between knowledge of the subject matter by teachers and academic performance of students (r=0.526**, p<0.01) and a statistically moderate positive and significant relationship between method of teaching by teachers and academic performance of students (r=0.566**, p<0.01) in Uganda Certificate of Education in public secondary schools in Kisoro district. The study recommended that there is need to regular supervision of both teachers and students by administrators and this would cause teachers to concentrate on improving academic performance; and that teacher’s method of teaching be improved to change the academic performance of students in Uganda Certificate of Education in public secondary school in Kisoro district.