This study was conducted to investigate the intricate relationship between school population and students’ academic progress within the context of Universal Primary Education (UPE) at Muko Primary School in Kisoro District, Uganda. The research was guided by three specific objectives: to determine the level of school population, to establish the level of students’ progress, and to examine the relationship between these two variables. A descriptive research design was adopted, employing both quantitative and qualitative data collection methods from a sample of 240 respondents, including administrators, teachers, and students, selected through simple random and purposive sampling techniques. Data were gathered using questionnaires and interview guides, and analyzed using descriptive statistics and content analysis. The results revealed a critically high and unsustainable level of school population, characterized by severe congestion and a pupil-teacher ratio that far exceeded national standards. This high population was found to be a significant positive predictor of overall enrollment but was negatively associated with infrastructure adequacy. Furthermore, the level of students’ progress was established to be critically low. Multiple linear regression analyses identified a statistically significant negative relationship between school population metrics and academic achievement. Specifically, the total school population, pupil-teacher ratio, and classroom density were all significant negative predictors of students’ progress scores, confirming that overcrowding directly and substantially impedes learning outcomes. The study concluded that Muko Primary School is trapped in a cycle of educational inefficacy, where the quantitative success of UPE in boosting enrollment has directly precipitated a qualitative crisis in learning. The high student population overwhelms the available human and physical resources, creating a learning environment that is fundamentally hostile to academic achievement. It was recommended that a multi-pronged approach is urgently needed. This includes immediate government action to recruit more teachers and construct new classrooms, the implementation of internal efficiency measures like a double-shift system by the school administration, and active advocacy and partnership from parents and the community. A paradigm shift from a focus on mere enrollment to a balanced agenda prioritizing educational quality is essential to break the cycle of congestion and poor performance.