We report a rare case of ectopic ureter accompanied by a giant ureteral stone and pyonephrosis. A 19-year-old Japanese woman consulted our hospital due to low-grade fever and pain in the left flank. The patient had seeping urinary incontinence since childhood. Ultrasonography demonstrated left dysplastic lumbar kidney with hydronephrosis and plain kidney-ureter-bladder film showed a left giant ureteral stone. The left kidney showed no excretion of contrast medium on drip infusion pyelography. After further examination, a diagnosis of left simple ectopic ureter emptying into the vagina was made. Percutaneous nephrostomy penetrating the major psoas muscle was carried out for intractable pyonephrosis, followed by left nephroureterectomy and lithectomy. These procedures resulted in improvement in the patient's symptoms.