Stenotrophomonas maltophilia is an important nosocomial pathogen, especially among immunocompromised patients. The objective of this study was to clarify the clinical characteristics, prognosis, and prognostic factors of patients with S. maltophilia bacteremia in Japan. The microbiology records of all patients with S. maltophilia bacteremia between January 1996 and April 2009 at Toranomon Hospital, Tokyo, Japan, were retrospectively reviewed. A total of 53 cases of bacteremia were identified. Thirty patients had an underlying hematological disorder, and 23 were receiving hematopoietic transplantation. The overall mortality rate was 51%. On univariate analysis, neutropenia (p < 0.01), the presence of a central venous catheter, and mixed infection with enterococci (p < 0.05) were significantly related to the mortality. Among these variables, neutropenia (p < 0.01) and mixed infection with enterococci (p < 0.05) were independent factors associated with mortality. In contrast, all eight patients in whom S. maltophilia was the etiologic agent of catheter-related infection survived following catheter removal. S. maltophilia is an important pathogen among immunocompromised patients, especially in the neutropenic phase or mixed infection with enterococci. If a central venous catheter was present at the onset of S. maltophilia bacteremia, the prompt removal of the catheter was important.