This study examined the relationship between staff discipline and pupils’ academic performance at the Primary Leaving Examination (PLE) level in selected primary schools of Nyakinama Sub-County, Kisoro District, Uganda. A descriptive cross-sectional research design employing both quantitative and qualitative approaches was adopted. Data were collected from 140 respondents comprising teachers, head teachers, and district education officials using questionnaires and interview guides. Quantitative data were analyzed using descriptive statistics and Pearson’s correlation coefficient, while qualitative data were analyzed thematically. The findings revealed a positive but weak and statistically significant relationship between staff discipline and pupils’ academic performance at PLE level (r = 0.212, p < 0.05). Key indicators of staff discipline, including punctuality, regular attendance, lesson preparation, and adherence to professional ethics, were found to contribute to a conducive learning environment; however, they accounted for only a limited proportion of variation in pupils’ academic performance. The study concludes that staff discipline plays a supportive rather than dominant role in enhancing pupils’ academic performance. It therefore recommends strengthened supervision, continuous professional development, and the adoption of holistic interventions that address multiple determinants of learner achievement.