Background: Treatment of upper urinary tract stones measuring >2 cm in children aged <3 years is challenging. Although adult-sized instruments are usually available, in pediatric populations such instruments seem unreasonable and unfit for children with small kidneys and narrow ureters. We use ultra-miniaturized endoscopes and instruments to reduce the damage to normal tissues in pediatric patients. Case Presentation: We treated a 2-year-old boy with >2-cm bilateral cystine kidney stones. We decided to perform retrograde intrarenal surgery using an ultrathin (4.5F) semi-rigid ureteroscope for the right kidney stone (2.0 × 1.2 cm) in the lithotomy position and super ultra-minimally invasive endoscopy combined with intrarenal surgery with a percutaneous 8.5F to 9.5F tract sheath for the left kidney stone (3.5 × 2.4 cm) under the Barts modified Valdivia position. These procedures were successful for the bilateral kidney stones. Postoperatively, the patient was stone-free without major complications. Conclusion: We believe that ultra-minimally invasive endoscopic intrarenal surgery is safe and efficient in pediatric patients. Furthermore, the Barts modified Valdivia position was safely utilized in our 2-year-old patient with multiple large kidney stones.