Granulomatous appendicitis is a very rare entity in children. It is related to Crohn’s disease in only 5-10% of the cases. The diagnosis of Crohn’s disease is a real challenge in the pediatric population, especially when its initial manifestation is acute appendicitis. Herein, we present a 13-year-old boy admitted for acute appendicitis. The histopathological examination was conclusive for acute granulomatous appendicitis. The development of an entero-cutaneous fistula has complicated the postoperative evolution. The failure of the conservative management required ileocecal resection. The pathological examination revealed Crohn’s disease. The one-year follow-up on the patient din not reveal any complications. We strongly support the importance of the histopathological examination of the entirely removed appendix. Careful assessment of granulomatous appendicitis is needed in order to establish its possible etiology and to initiate the adequate treatment.