The purpose of the study was to establish the physical and learners’ academic performance in secondary schools at St. Charles Lwanga. The study was set up to examine the physical education and learner's academic performance in secondary school a case study St. Charles Lwanga secondary school. The specific objectives of the study were to (i) examine the impacts of Physical Education on learner's academic performance in St. Charles Lwanga secondary school; (ii) determine the challenges faced by both students and teachers during Physical Education in St. Charles Lwanga secondary school; (iii) investigate the solutions to the challenges faced by the students and teachers during Physical Education in St. Charles Lwanga secondary school. This study employed a cross sectional survey design. Access population comprised of 100 respondents consisted of 1 head teacher, 5 teachers, 85 learners and 5 parents. The main data collection tools were questionnaire and interview guides. This helped to gather quantitative and qualitative information which were coded and measured. The study revealed a significant of physical education and learners academic performance used in selected schools and learners performance but was not strong enough to eliminate poor performance of learners. The study concluded that the physical education and learners academic performance that were used in selected schools was positive and significant. The research recommended that there is need to motivate teachers so that physical education activities are conducted well in schools and Teachers who have knowledge on physical education should be employed in schools for better skills imparting.