Clear cell adenocarcinomas similar to those found in the female genital organs can arise in the lower urinary tract of both women and men. Clear cell adenocarcinomas occurring in the upper urinary system are exceedingly rare. Here, we present a case of clear cell adenocarcinoma arising from the upper ureter and renal pelvis of a postmenopausal woman with a ureteral stone. The patient had elevated serum levels of cancer antigen (CA) 125 (103.80 U/mL) and CA19-9 (151.96 U/mL). The tumor showed typical features of tubulopapillary structures lined with clear-to-eosinophilic cytoplasm and frequent hobnail configuration. The tumor cells were immunoreactive for cytokeratin 7, cytokeratin 20, carcinoembryonic antigen and CA125, but negative for PAX-2 and alpha-methylacyl coenzyme A racemase. Given the presence of intestinal and squamous metaplasia of the adjacent urothelium, we propose that this clear cell adenocarcinoma developed through a metaplastic process. The tumor behaved so aggressively that the patient developed multiple metastases and died of the disease 5 months after radical nephroureterectomy.