A 3-year-old girl with acute myeloid leukemia underwent unrelated cord blood stem cell transplantation (UCBT) due to primary induction failure. Fourteen days after UCBT, she developed central venous catheter (CVC)-related bloodstream infection due to Chryseobacterium indologenes. Despite ciprofloxacin and minocycline being administered according to the results of susceptibility, a high grade fever recurred. Therefore, the CVC was removed 21 days after UCBT and symptoms related to CVC infection improved. Although C. indologenes is widely distributed in nature, it is a rare pathogen in humans. Most cases of C. indologenes bacteremia have been found in immunocompromised patients with malignancies and diabetes mellitus. C. indologenes exhibits specific characteristics, including the progression of resistance to antibiotics and the formation of a biofilm. Therefore, removal of the CVC appears to be the most reasonable treatment for CVC infection due to C. indologenes in patients undergoing hematopoietic stem cell transplantation if clinical symptoms do not improve after appropriate antibiotic therapy.