A 14-year-old boy was admitted to a general hospital because of prolonged fever of unknown origin. After Enterococcus feacalis was detected from his urine and abdominal contrast enhanced computed tomography and 99m-Tc dimercaptosuccinic acid scintigram showed multiple focal defects, he was diagnosed as acute focal bacterial nephritis (AFBN). His condition recovered as a result of Ampicillin (ABPC)and Cefotaxime infusion. There was no specific finding in voiding cystography. Six months later, his fever recurred and he was diagnosed as refractory AFBN because Enterococcus feacalis was detected in his urine again. He was treated with ABPC and Meropenem (MEPM) infusion, but the fever persisted and his renal function deteriorated. He was transferred to our hospital for intensive treatment. On admission, blood examination showed findings of inflammation (WBC 14,400/μL, CRP 3.7 mg/dL, erythrocyte sedimentation rate : 69 mm/h, IgG : 2,107 mg/dL) and renal impairment (Cr : 1.8 mg/dL, cystatin C : 2.0 mg/L). Although neither pyuria nor pathogenic bacteria were detected in his urine, Enterococcusfeacalis was detected at the hospital where he had been treated previously, hence we started treatment for AFBN with ABPC, MEPM, Levofloxacin, then Linezolid. However, the fever persisted and his renal function deteriorated (Cr 2.0 mg/dL). Kidney-specific accumulation was found in Ga scintigraphy, which suggested chronic inflammation. Clinical course and laboratory findings showed no symptoms of bacterial, viral, fungal, or tuberculous infections nor collagen disease. Although renal biopsy revealed no glomerular abnormality, tubulointerstitial edema, fibrosis and tubulitis were observed. Rupture of the tubular basal membrane and non-caseating granulomas also existed. Pathological findings did not match those of renal sarcoidosis. Ophthalmological screening negated the existence of tubulointerstitial nephritis with uveitis syndrome. After methylprednisolone pulse therapy, the fever recovered immediately and his renal impairment imroved gradually (Cr 1.49 mg/dL). He continues to undergo treatment as an outpatient. Although tubulointerstitial nephritis is rare in children, some patients have a poor renal prognosis. It is important to determine the existence of tubulointerstitial nephritis on treating a patient with renal impairment.