Background: Misdiagnosis and delayed treatment of hypothyroidism can lead to irreversible complications in children. Objectives: This study aimed to compare the neurodevelopmental status of children with congenital and acquired hypothyroidism. Methods: A retrospective cohort study was conducted in Tehran, Iran (2021 - 2022), involving children aged 3 - 5 years diagnosed with hypothyroidism. Participants were divided into two groups based on medical records: Congenital and acquired hypothyroidism. Neurodevelopmental status was assessed using the Ages and Stages Questionnaire (ASQ). Final scores above -1 SD and below -2 SD were considered as normal and abnormal neurodevelopmental status, respectively. The frequency of abnormal neurodevelopmental status was compared between the groups. Results: The frequency of delayed neurodevelopmental status was higher in the congenital hypothyroidism group than in the acquired group; however, the difference was not statistically significant. In the congenital group, the age of diagnosis was significantly associated with delays in communication (P = 0.03), gross motor (P = 0.03), fine motor (P = 0.04), and problem-solving (P = 0.02) domains. Significant associations were also observed between low levels of free T4 and delays in communication (P = 0.04), gross motor (P = 0.04), and problem-solving (P = 0.02) skills. Maternal hypothyroidism during pregnancy was significantly associated with abnormal personal-social behavior (P = 0.02). Conclusions: Although the frequency of neurodevelopmental abnormalities was higher in the congenital hypothyroidism group compared to the acquired group, the difference was not significant. The comparable risks for neurodevelopmental abnormalities in both congenital and acquired hypothyroidism groups suggest the need for increased attention and interventions to prevent adverse outcomes. Further studies with larger sample sizes are required to confirm these findings.