We experienced a case of squamous metaplasia mimicking papillary urothelial cell carcinoma in the upper urinary tract. A 69-year-old woman, who complained of gross hematuria and intermittent left flank dull pain underwent nephrectomy with the clinical diagnosis of papillary urothelial carcinomas in the left upper urinary tract according to positive split urine cytology and tumorous filling defects of contrast media by the abdominal CT scan. Pathological diagnosis was squamous metaplasia and concomitant foreign body granuloma. Those changes were judged due to a tiny calculus in the ureter. Our presented case implies that a tiny calculus can cause the metaplastic change in the urothelial epithelium and the combination of radiographical and cytological diagnoses would not be enough to lead the correct diagnosis and the definitive surgical treatment against protruding lesions in the upper urinary tract requires more reliable diagnostic modalities.