The study aimed at the effects of physical education on the learner’s academic performance in secondary school and it was guided by the following objectives; To investigate the relationship between physical education and students’ performance in kabojja secondary school, to analyze the contributions of physical education to the students’ performance in kabojja secondary school and to examine the relevance of physical education to the academic performance in kabojja secondary school. The results of the descriptive and inferential statistical analyses were displayed via tables, figures, and proportions. Utilizing an analytical methodology, the qualitative information was examined for any emerging patterns in the responses given by the participants. From the findings, it was found that learners and their skeletal muscles are at ease and their minds are enhanced by the exercises that they practice in middle and high schools, as pointed out with 27% of the teachers, while the greatest number of educators said that pupils are apprised of athletic endeavors during physical schooling this has been demonstrated with 32%, while it was also noted throughout the survey that learners have learned to relate science lessons with wellness as shown with. Engaging in physical activities during physical education classes can enhance cognitive functions such as attention, memory, and problem-solving skills. Schools should design physical education programs that include activities that stimulate the brain and require critical thinking.