Enterococcus hirae mainly causes infections in animals. It has been rarely encountered in humans and, in most such cases, it is considered to be a contaminant or resident flora. Since the first case of septicemia by E. hirae was reported in 1998, only two cases of acute pyelonephritis (APN) have been reported in Korea. We describe herein a case of APN caused by E. hirae in an 83-year-old man with a horseshoe kidney. Although E. hirae was isolated only from urine and not from the blood, we were able to diagnose it as the causative organism based on the patient’s clinical findings, imaging study results, and risk factors including old age, benign prostatic hypertrophy, and a horseshoe kidney.