Alport syndrome (AS) is a rare genetic disorder that causes progressive nephritis and is more common among males. Studies have reported an association between thyroid antibodies and hypothyroidism in patients with AS, but the relevance of this relationship is under debate. Prolonged untreated hypothyroidism induces short stature, abnormal pubertal development, and various other symptoms. However, children with long-standing hypothyroidism rarely present with signs of precocious puberty, or Van Wyk-Grumbach syndrome (VWGS). We report the case of a boy, 8 years and 4 months old, who had VWGS caused by prolonged untreated congenital hypothyroidism and AS. The boy had repeated gross hematuria and proteinuria and was diagnosed with AS by renal biopsy and genetic testing. He had normal renal function but severe growth retardation and hypothyroidism. Obesity, bone age delay, hyperlipidemia, and abnormal increased testicle size were also present due to prolonged untreated hypothyroidism. His thyroid antibody titer elevation was unclear, although ultrasonography and thyroid scanning showed a decrease in thyroid volume. We diagnosed the patient with congenital hypothyroidism caused by thyroid dysgenesis. VWGS was diagnosed due to hypothyroidism, delayed bone age, and pseudoprecocious puberty. To the best of our knowledge, this is the first report of a prepubertal Korean boy with prolonged untreated congenital hypothyroidism complicated by VWGS in AS.