While endoscopic subureteral injection of bulking agents has become a first-line therapy for the treatment of vesicoureteral reflux (VUR), mainly due to its high success rates with minimal complications, polydimethylsiloxane (PDS) administration can be associated with bladder calcification in a minority of patients. A 10-year-old girl with prior history of subureteral administration of PDS as a treatment modality for bilateral VUR six years ago showed recurrent lower urinary tract symptoms, including dysuria, frequency, and urgency, for the past 6 months. She was admitted to our institution for right pyelonephritis with hydronephrosis. Radiologic examination had revealed two yellowish impacted stones attached to the previous site of PDS administration without recurrence of VUR. The stones were completely removed by cystolitholapaxy. This study suggests that such a late-complication should be considered in patients with recurrent urinary tract infection or lower urinary tract symptom despite complete disappearance of VUR by prior subureteral administration therapy.