This study examined the influence of child neglect on the academic performance of pupils in government primary schools in Bundibugyo District, Uganda. Child neglect—the failure to provide for a child's basic physical, educational, emotional, and supervisory needs—is among the most common yet under-recognised forms of child maltreatment, and it has serious consequences for children's learning. The study investigated how physical neglect, educational neglect, emotional neglect, and supervisory neglect relate to pupils' academic performance. A cross-sectional survey design with a mixed-methods approach was adopted, and data were collected from 190 respondents comprising teachers, head teachers, parents and guardians, and education officials using structured questionnaires and interviews. Descriptive statistics, exploratory factor analysis, Pearson correlation, and structural (path) analysis were used. Factor analysis confirmed the construct validity of the neglect dimensions, which loaded onto coherent factors and explained 67.6% of the variance. The results revealed a strong negative and significant relationship between child neglect and academic performance (r = −0.66, p < 0.01), with the neglect dimensions jointly explaining 64.0% of the variance in academic performance (R² = 0.640). Educational neglect (β = −0.32) and physical neglect (β = −0.28) emerged as the strongest path predictors. The study concludes that child neglect significantly impairs academic performance and recommends child-protection interventions, parental sensitisation, and school-based support. This study addresses a sensitive topic in an academic manner, with attention to the wellbeing and protection of children.