Early deprivation holds far-reaching implications for academic performance in adolescence. Yet, the implicated cascading mechanisms remain under-delineated, and little is known about why children may display diverse patterns of cognitive development. To address such gaps, we leveraged long-term longitudinal data derived from the Future of Families and Child Wellbeing Study (n = 2,085). Results indicated that early deprivation (age 3, caregivers’ reports and observers’ ratings; controlling for early threat and unpredictability) was negatively associated with adolescent academic performance (age 15, adolescents’ reports) indirectly through a negative association with cognitive ability in middle childhood (age 9, standardized tests). Furthermore, such an indirect effect was less pronounced among children with higher (versus lower) negative emotionality (age 1, mothers’ ratings), given that the negative link between early deprivation and subsequent cognitive ability was weaker among children with higher (versus lower) negative emotionality. Breaking down cognitive ability into sub-components (i.e., working memory, language ability, reading comprehension, and problem-solving), both language ability and applied problem-solving were involved in the deprivation-emotionality interaction. These findings highlight the critical role of cognitive ability in accounting for the long-term academic consequences of early deprivation and the key role of negative emotionality in shaping heterogeneity in such pathways.