Haemophilus species are known to colonize the upper respiratory tract and can cause infections. However Haemophilus influenzae has been rarely described as a cause of genitourinary tract infection. We report a 44-year-old nonimmunocompromised Japanese man with bacteremic pyelonephritis caused by a nontypable H. influenzae associated with a left ureteral calculus. The organism was isolated from both blood and urine cultures. Treatment consisted of 14 days of intravenous ceftriaxone and oral amoxicillin one after than other and insertion of a left ureteral stent. After discharge, he underwent extracorporeal shock wave lithotrity for the left ureteral calculus. He had no recrudescence of the symptoms. H. influenzae should be considered as a genitourinary pathogen among patients with certain risk factors such as anatomical or functional abnormality of genitourinary tract. Collaboration between clinicians and microbiology laboratory personnel is essential for correct identification of the organism and appropriate therapy for genitourinary tract infections due to this organism.