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Background: Since 1990, neonatal, infant, and child mortality has substantially decreased in Iran. However, estimates for mortality by cause at subnational scale are not available. Methods: This study is part of the Global Burden of Diseases, Injuries, and Risk Factors study (GBD) 2019. Here we report the number and rates of neonate, infant, and child deaths by cause across provinces of Iran from 1990 to 2019. Results: Between 1990 and 2019, the neonatal mortality rate per 1000 live births decreased from 31.8 (95% UI: 28.1–35.5) to 6.8 (6.1–7.4). The child mortality rates decreased from 71.2 (63.6–79.1) to 11.1 (10.2–12.0) per 1000 live births. Mortality rates among neonates per 1000 live births ranged from 3.1 (2.6–3.7) to 10.0 (9.2–10.8) across provinces in 2019. Child mortality rate per 1000 live births ranged from 5.5 (4.6–6.5) to 17.9 (16.4–19.4) across provinces in 2019. Neonatal disorders, congenital birth defects, and lower respiratory infections were the three main causes of mortality in almost all provinces of Iran. The majority of neonatal disorders were due to neonatal preterm birth and neonatal asphyxia, trauma, and infections. The trends of mortality across provinces from 1990 to 2019 were converging and decreased along with increase in sociodemographic index (SDI). Conclusions: All provinces achieved the Sustainable Development Goal 3.2 of neonatal mortality less than 12 and child mortality less than 25 per 1000 live births. However, disparities still exist across provinces, specifically in low-SDI provinces.