We investigated inequalities in learning achievements at 12 years by household food insecurity trajectories at ages 5, 8 and 12 years in a longitudinal sample of 1,911 Indian children. Estimates included extensive child and household controls, and lagged cognitive scores to address unobserved individual heterogeneity in ability and early investments. Overall, household food insecurity at any age predicted lower vocabulary, reading, maths and English scores in early adolescence. Adolescents from households that transitioned out from food insecurity at age 5 to later food security, and adolescents from chronically food insecure households had the lowest scores across all outcomes. There was heterogeneity in the relationship between temporal occurrence of food insecurity and cognitive skills, based on developmental and curriculum-specific timing of skill formation. Results were robust to additional explanations of the “household food insecurity gap”, i.e. education and health investments, parental and child education aspirations, and child psychosocial skills.