We report the case of a 56-year-old postmenopausal woman who presented with incidental left hydronephrosis during an investigation for a gastrointestinal complaint. The patient denied any history of flank pain or hematuria. Contrast-enhanced computed tomography revealed severe right-sided ureterohydronephrosis as well as renal atrophy. The contralateral kidney was normal, as was the patient's overall renal function. A retrograde ureterogram demonstrated complete ureteral obstruction 4 cm proximal to the ureterovesical junction. Subsequent ureteroscopy revealed a polypoid mass completely occupying the ureteral lumen, of which the biopsies demonstrated inconclusive atypical urothelial changes. The patient underwent a laparoscopic nephrectomy with open dissection of the distal ureter. The patient recovered well postoperatively. Final pathology revealed a benign obstructing endometrioma without evidence of invasion from periureteral tissue. This appears to be the first reported case of asymptomatic primary ureteral endometrioma with secondary renal atrophy. Earlier investigation and treatment may have allowed for renal preservation earlier in the course of the disease.