Background: Neutropenic enterocolitis is a devastating bowel wall inflammation in patients with protracted neutropenia. The approach for diagnosis and treatment is still controversial, and it is difficult and challenging to decide on what should be the next step in the management. Case presentation: We report a 10-year-old boy who developed neutropenic enterocolitis in the course of the conservative treatment for aplastic anemia. Oral mucositis and the perianal fissure with an ulcer were important indicators for what was happening on the colonic mucosa. Colonoscopy and biopsy confirmed the diagnosis. A fast recovery was achieved with a right hemicolectomy and ileostomy. Conclusion: Retrospective analysis of the long-term follow-up of our patient suggests that defunctioning the colon by ileostomy breaks the vicious circle between neutropenia and bowel wall inflammation, and an early surgical intervention could be considered as an adjunctive approach to the conservative management of persistent cases.