Background: In Pakistan, nearly half of children younger than 5 years are stunted, and 1 in 3 is underweight. Micronutrient deficiencies, a less visible form of undernutrition, are also endemic. They may lead to increased morbidity and mortality as well as to impaired cognitive and physical development. Objective: To estimate the lifetime costs of micronutrient deficiencies in Pakistani children aged between 6 and 59 months. Methods: We develop a health economic model of the lifetime health and cost consequences of iodine, iron, vitamin A, and zinc deficiencies. We assess medical costs, production losses in terms of future incomes lost, and disability-adjusted life-years (DALYs). The estimation is based on large population surveys, information on the health consequences of micronutrient deficiencies extracted from randomized trials, and a variety of other sources. Results: Total societal costs amount to US$46 million in medical costs, US$3,222 million in production losses, and 3.4 million DALYs. Costs are dominated by the impaired cognitive development induced by iron-deficiency anemia in 6-to 23-month-old children and the mortality caused by vitamin A deficiency. Costs are substantially higher in poorer households. Conclusions: Societal costs amounted to 1.44% of gross domestic product and 4.45% of DALYs in Pakistan in 2013. These costs hinder the country's development. They could be eliminated by improved nutrition of 6-to 59-month-old children and public health measures. Our results may contribute to the design of cost-effective interventions aiming to reduce micronutrient deficiencies in early childhood and their lifetime consequences.