This study examined the relationship between teacher motivation and the academic performance of learners in government-aided primary schools in Mbarara District, Uganda. Motivated by persistent concerns about declining performance at the Primary Leaving Examination (PLE) level, the study investigated how intrinsic and extrinsic motivational factors—remuneration, working conditions, professional development, recognition, and school leadership support—relate to pupils' learning outcomes. A cross-sectional survey design combining quantitative and qualitative approaches was adopted. Data were collected from a sample of 210 teachers and 30 head teachers drawn from 40 government-aided primary schools using structured questionnaires and interview guides. Descriptive statistics, Pearson correlation, and multiple linear regression were used to analyse the data. Results revealed a positive and statistically significant relationship between teacher motivation and learners' academic performance (r = 0.62, p < 0.01). Regression analysis indicated that teacher motivation explained approximately 48.6% of the variance in academic performance (R² = 0.486), with remuneration and working conditions emerging as the strongest predictors. The study concludes that improving teacher motivation is central to raising pupil achievement and recommends that the Ministry of Education and Sports, district authorities, and school managers prioritise timely payment of salaries, provision of adequate teaching materials, and structured recognition schemes.