The study established the relationship between pupils’ discipline and pupils’ academic performance in primary schools in Rwamucucu subcounty, Rukiga district, Uganda. It used convergent parallel mixed methods, by merging quantitative and qualitative data thus making easy all-encompassing analysis of the research problem. A sample size of 248 respondents was considered for the study, 186 respondents participated, giving a response rate of 75%. The study established a moderate significant correlation coefficient between academic performance and pupils' discipline is also reported as 0.569. Therefore, it was recommended to invest in specialized training equipping teachers with an array of preventative and restorative methods proven to effectively counteract misconduct while repairing relationships and maintaining student engagement represents another intervention strongly recommended as well as establishing collaborative structures empowering parents and community members as partners in supporting conduct maintenance both inside and beyond school gates also deserves consideration.