Congenital disorders of glycosylation (CDG) are a heterogeneous group of inherited metabolic diseases (IMD) characterized by defects in the synthesis and modification of glycoproteins and glycolipids. One of these disorders is ATP6AP1-CDG, a rare X-linked disease with approximately 30 cases reported so far. Symptoms associated with ATP6AP1-CDG include immunodeficiency, liver dysfunction, and neurological manifestations. This report presents the first case of ATP6AP1-CDG in Iran and the Middle East, in a 5-month-old male infant presenting with fever, vomiting, diarrhea, and poor feeding.