Acrodermatitis enteropathica is a rare genetic metabolic disorder affecting the absorption of zinc ions in the digestive tract. The classic clinical manifestation of zinc deficiency, seen in about 20% of cases, is the triad of symptoms: acral and periorificial dermatitis, diarrhoea, and alopecia. This case report of a 16-month-old girl with an atypical course of acrodermatitis enteropathica posed a diagnostic challenge for clinicians. The first skin lesions appeared after infancy and initially presented as blisters; later, the patient developed a more severe clinical picture including erythematous plaques, paronychia, and alopecia. Zinc serum levels were within reference ranges. Genetic testing showed a pathogenic mutation characteristic of acrodermatitis enteropathica in the SCL39A4 gene. Marked improvement in the healing of skin lesions was observed only after the initiation of oral zinc supplementation. Making a proper diagnosis in cases of metabolic disorders can significantly improve the patient’s quality of life and prevent distant consequences, such as mental and physical retardation.