Carbapenem-resistant Enterobacteriaceae (CRE) are resistant to almost all β-lactam antibiotics. Colistin,the production of which had been halted in Japan because of its serious side effects and the availability of safer alternatives, was re-evaluated as an antibiotic against CRE and re-approved in March 2015. However,the pediatric use of colistin has been reported in only few studies. A 4-year-old girl with juvenile myelomonocytic leukemia underwent stem cell transplantation (SCT) from her mother after the rejection of umbilical cord blood transplantation. Two months after engraftment, her neutrophil count gradually decreased. She developed sepsis caused by carbapenem-resistant Escherichia coli with severe neutropenia. Although multidrug therapy was initiated, E. coli continued to be detected in her blood cultures. We initiated colistin as an emergency measure and infused it into the patient at a dose of 5mg/kg/day. Despite clinical and microbiological responses and an immediate negativity of blood cultures, she redeveloped a high fever, and E. coli was again detected in her blood cultures. The colistin dose was increased to 7mg/kg/day. Neutrophils from her father were transfused after the patient had the central venous catheter was removed. Eventually,her temperature normalized, and her blood cultures became negative again. Colistin was administered for 14 days. No side effects related to colistin were detected. It is suggested that colistin in multidrug therapy can be safely and effectively used for children with severe CRE infections.