Polyarteritis nodosa (PAN) is a rare systemic necrotizing vasculitis affecting small- to medium-sized arteries. The most common gastrointestinal manifestation of PAN is postprandial abdominal pain from mesenteric arteritis causing bowel ischemia. When transmural ischemia develops, there may be ischemic necrosis and perforation of the bowel wall, which are life-threatening. Severe, life-threatening gastrointestinal involvement is relatively rare in pediatric PAN and may require different management in adult patients. We report a pediatric PAN case in a patient who presented with acute abdominal pain and superimposed cytomegalovirus enteritis with jejunoileal perforation. The patient improved with emergency small intestinal resection followed by conventional immunosuppressive drugs of a corticosteroid and cyclophosphamide, and anti-viral drugs. Before increasing the immunosuppressive drug dosage, initial screening of infectious cytomegalovirus and comprehensive evaluation for surgical conditions are essential in pediatric PAN with severe gastrointestinal involvement. Early aggressive treatment for acute abdomen is useful in reducing morbidity and mortality in pediatric PAN.