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Despite significant advancements in the early detection and treatment of congenital hypothyroidism (CH), a developmental and growth gap persists between affected children and their healthy peers. This study aims to assess some growth and developmental aspects among a sample of Egyptian children who had CH and were subjected to the recommended national CH treatment program, with a focus on age- and gender-related differences. A prospective case-control follow-up study was conducted from February 2021 to February 2023 in Giza Governorate, Egypt, involving 80 children aged 1.5–3 years, including 40 with CH (Group A) and 40 age- and gender-matched healthy controls (Group B). CH was diagnosed at birth via newborn screening and confirmed by elevated TSH and low free T4 levels. Participants underwent two follow-up assessments: the first one year after initiation of thyroid hormone therapy and confirmation of treatment adherence, and the second one year later. During each follow-up, clinical, laboratory, growth, and developmental evaluations were conducted using CDC growth charts, PLS-4 (Arabic Version), Stanford-Binet 5th Edition, and Portage Program Questionnaire. By the second follow-up, children with CH showed significant delays across all developmental domains compared to controls (p ≤ 0.001). Female children with CH exhibited earlier language delays—both receptive (p = 0.025) and expressive (p = 0.015)—during the first follow-up. In the second follow-up, girls continued to show deficits in height, weight, and receptive language age, although expressive language showed signs of improvement. Male children demonstrated more pronounced growth and developmental compromise during the second follow-up, with significant deficits in height (p = 0.001), weight (p = 0.016), and receptive language age (p = 0.001). An inverse correlation was observed between receptive language age and CH status. Children with CH continue to face developmental and growth challenges despite adherence to standard treatment protocols. Delays appear earlier in girls, particularly in language domains, whereas boys tend to show more pronounced deficits with increasing age. These findings indicate a distinct gender-based developmental pattern in children with CH, emphasizing the importance of sex-specific monitoring and timely interventions to optimize long-term outcomes.