For the management of patients with cystinuria, forced hydration and medication have been used to prevent stone recurrence and growth, but not a few cystine stones require surgical intervention. However, the long-term follow-up data about surgical intervention for cystine stones is lacking. Here, we report a case of cystine calculi of cystinuria with many sessions of extracorporeal shock wave lithotripsy (ESWL) during the long-term follow-up period. A 13-year-old woman went to a local clinic with right flank pain in January 1993, and abdominal ultrasonography revealed right kidney stones. She was admitted to our hospital for treatment using ESWL. Analysis of the stone components revealed the stone to be composed of cystine. During the next 25 years, she received 157 sessions of ESWL and 2 sessions of transurethral ureterolithotripsy (TUL). Current examination revealed that although the lower pole of her right kidney is slightly atrophic, her renal function is stable and kidney stones remain small. Our case suggests that early intervention by ESWL could prevent stone growth and the deterioration in renal function.