Cystinuria is a disease characterized by impaired reabsorption of cystine and other dibasic amino acids. In this paper, we report a case diagnosed with cystinuria after multiple surgical interventions. A 16-year-old girl with a history of recurrent kidney stones admitted to Pediatric Nephrology Clinic. Her medical history revealed kidney stones detected at the age of one year, after that she had multiple surgical interventions, including nephrectomy. Direct microscopic examination of the urine revealed cystine crystals. Cystinuria was considered due to positive urinary cystine and dibasic amino acid excretion. She was recommended dietary sodium restriction and hydration. The patient was followed up without the formation of new kidney stones after the 12th month of her treatment. The etiology of the stone should be investigated in patients with recurrent urinary stones. Chronic kidney disease and associated morbidity and mortality can be prevented in patients with regular follow-up and treatment that will prevent stone formation.