This study examined the effect of early neglect on cognitive functioning among children in orphanages in Wakiso District, Uganda. Grounded in evidence that early experiences shape brain development, the study investigated how dimensions of early neglect—emotional neglect, cognitive and educational neglect, physical and nutritional neglect, and lack of stable caregiving—relate to children's cognitive functioning. A cross-sectional survey design with a mixed- methods approach was adopted, and data were collected from 160 respondents comprising caregivers, orphanage administrators, and teachers who reported on 160 children, using structured questionnaires, standardised assessment indicators, and interviews. Descriptive statistics, Pearson correlation, and multiple regression were used for analysis. The results revealed a strong negative and significant relationship between early neglect and cognitive functioning (r = -0.66, p < 0.01), with the dimensions of neglect jointly explaining 51.1% of the variance in cognitive functioning (R² = 0.511). Cognitive and educational neglect and lack of stable caregiving were the strongest predictors. The study concludes that early neglect significantly impairs children's cognitive functioning and recommends stable caregiving, stimulation-rich environments, and early intervention. This is a sensitive topic; where children's welfare is a concern, professional support should be sought.