This study investigated the effects of physical education (PE) on learners' academic performance in secondary schools, focusing on Kabojja Secondary School. Specifically, the study aimed to explore the relationship between physical education and students’ performance, analyze the contributions of PE to academic outcomes, and examine its relevance to academic achievement. A cross-sectional design was adopted, and data were collected through structured questionnaires administered to students and teachers. Multiple logistic regression analysis was employed to determine significant predictors of academic performance using SPSS and STATA software. The results revealed that regular participation in physical education significantly enhanced students’ academic performance. The odds ratio for the frequency of PE participation was 2.34 (p < 0.05), indicating that students engaged in regular PE were more than twice as likely to perform better academically. Similarly, time spent on PE showed an odds ratio of 1.70 (p < 0.05), demonstrating its positive contribution. Team sports and regular fitness assessments emerged as significant contributors to improved academic outcomes, with odds ratios of 2.15 and 1.89, respectively (p < 0.05). Furthermore, the relevance of physical education as perceived by students showed the highest impact, with an odds ratio of 2.77 (p < 0.01), emphasizing the importance of aligning PE activities with students’ academic and developmental needs. The study concluded that physical education is a critical component of holistic education that significantly influences academic performance. It recommended integrating structured PE programs into the school curriculum, promoting team sports and fitness programs, and enhancing teacher training to maximize the academic benefits of physical education. Awareness campaigns and curriculum reviews were also recommended to foster a positive perception of PE among students.