Isolated granulomatous inflammation of the appendix is extremely rare, and its etiology is still unknown. Thus, differentiating between idiopathic granulomatous appendicitis and isolated appendiceal Crohn's disease is difficult. We report a case of idiopathic granulomatous appendicitis with long-term follow-up after surgery. A 26-year-old woman was referred to our hospital for investigation of persistent right lower abdominal pain. Abdominal computed tomography showed a mass, suggesting an inflammatory tumor around the appendix; thus, we suspected subacute appendicitis and performed laparoscopically assisted ileocecal resection. Histological examination of the resected specimen revealed several noncaseous epithelioid granulomas in the wall of the appendix, but no foreign bodies, obstructing lesions, or parasites. Stains for acid-fast bacillus and fungi, and serology for yersinia were all negative. The patient has been followed up for 9 years and remains asymptomatic. This clinical course suggests that her isolated granulomatous appendicitis was idiopathic granulomatous appendicitis unrelated to Crohn's disease.