Objectives To compare the outcomes of flexible ureteroscopy and mini-percutaneous nephrolithotomy for pediatric kidney stones larger than 2 cm and to show the learning curves for the two procedures. Methods A prospectively managed database containing pediatric patients with kidney stones larger than 2 cm from June 2014 to October 2019 was analyzed. The primary outcomes were the efficacy and safety of flexible ureteroscopy and mini-percutaneous nephrolithotomy. Data on patient demographics, treatment details, stone-free rate, and complication rate were collected and compared. Learning curves were generated to estimate the effect of the surgeon's experience on surgical outcomes. Results The final analysis included 113 pediatric patients who underwent surgery for kidney stones on a total of 126 sides. The stone-free rates for mini-percutaneous nephrolithotomy and flexible ureteroscopy were 80.9% (34/42) and 79.7% (67/84), respectively (P = 0.19). The complication rates for mini-percutaneous nephrolithotomy and flexible ureteroscopy were 52.5% (21/40) and 27.4% (27/73), respectively (P = 0.01). When stone mass was considered, the stone-free rates for mini-percutaneous nephrolithotomy and flexible ureteroscopy for stones with a high mass (>5000 HU*cm(2)) were 83.3% (20/24) and 55.5% (10/18), respectively (P = 0.04). The learning curves showed that the stone-free rates for both mini-percutaneous nephrolithotomy and flexible ureteroscopy increased with the accumulation of cases. A higher stone-free rate could be achieved after approximately 20 mini-percutaneous nephrolithotomy cases and after approximately 50 flexible ureteroscopy cases. Conclusions Flexible ureteroscopy has an acceptable stone-free rate and a lower complication rate than mini-percutaneous nephrolithotomy when treating pediatric kidney stones larger than 2 cm. Mini-percutaneous nephrolithotomy is more applicable to stones with a high mass. The stone-free rates achieved after both mini-percutaneous nephrolithotomy and flexible ureteroscopy could be improved with number of cases accumulated.