Pemphigus vegetans is a clinical variant of pemphigus vulgaris, accounting for 1–2% of all very rare pemphigus cases in children. The involvement of the oral mucosa in this disease is usually accompanied by severe pain that aggravates the patient’s malnourished condition. Conversely, malnutrition may also reduce vulnerability towards autoimmune diseases. Although pemphigus vegetans has never been reported to develop in a child with marasmus before, we encountered a case of pemphigus vegetans in a severely malnourished patient. A 12-year-old boy in marasmic condition presented with painful, clear, fluid-filled blisters, accompanied by erosions, crusts, and vegetative lesions on almost all parts of the body. Histopathological examination of the lesions revealed a suprabasal cleft, and direct immunofluorescence staining showed deposits of immunoglobulin G in the epidermal intracellular spaces. The patient was treated with a multidisciplinary approach, and intravenous corticosteroid was administered for 2 weeks with an appropriate diet. There were significant improvements in the skin lesions and his nutritional status. Although pemphigus vegetans may occur in children with malnutrition, the underlying mechanism for the development of autoimmune diseases in malnutrition remains unclear.