Bacteremic urinary tract infection (UTI) caused by Stenotrophomonas maltophilia rarely occurs in pediatric patients. We report a case of bacteremic UTI caused by S. maltophilia in an 8-month-old boy with a congenital ureteropelvic junction obstruction on the left side. The patient was brought to our hospital with a chief complaint of fever. He had undergone a nephrostomy tube insertion 4 months previously, and the tube had been removed 2 weeks before presentation at our hospital. He had a white blood cell count of 6,100/μL and a serum C-reactive protein level of 4.51 mg/dL. A microscopic urinalysis and Gram stain showed numerous Gram-negative bacilli and many leukocytes, and an ultrasonography showed grade 4 hydronephrosis of the left kidney. Based on these findings, we diagnosed the infant as having a complex UTI and started the intravenous administration of piperacillin/tazobactam. After 2 days, a urine culture showed Gram-negative bacilli (107 CFU/mL). Gram-negative bacilli were also cultured from two blood samples that were taken from different vessels at the time of admission. The Gram-negative bacilli were identified as S. maltophilia via the automated bacterial identification system. The patient recovered after a 2-week intravenous piperacillin/tazobactam treatment and subsequent oral treatment with trimethoprim-sulfamethoxazole. Since medical devices are susceptible to contamination with S. maltophilia, we suspect that the nephrostomy tube was the most likely source of infection.