Objectives To demonstrate the efficacy and safety of mini-percutaneous nephrolithotomy, micro-percutaneous nephrolithotomy, and flexible ureteroscopy for pediatric upper urinary tract calculi and to develop nomograms predicting surgical outcomes. Methods A prospectively managed database containing children who were diagnosed with upper urinary tract calculi and treated with mini-percutaneous nephrolithotomy, micro-percutaneous nephrolithotomy, and flexible ureteroscopy between June 2014 and April 2019 was analysed. Patient demographics, intraoperative data, stone characteristics, stone-free rate, and complication rate were analysed and compared. Nomograms predicting the postoperative stone-free rate and complication rate were established based on predictors, and internal validation was performed. Calibration curves and decision curves were generated to assess the predictive efficacy and clinical benefit. Results Forty-three children underwent mini-percutaneous nephrolithotomy on 56 sides in 47 operations, 30 children underwent micro-percutaneous nephrolithotomy on 30 sides in 30 operations, and 275 children underwent flexible ureteroscopy on 320 sides in 288 operations. The stone-free rates were 88.5% (282/320) for flexible ureteroscopy, 89.3% (50/56) for mini-percutaneous nephrolithotomy, and 90.0% (27/30) for micro-percutaneous nephrolithotomy (P = 0.94). And the complication rates were 19.8% (57/288), 36.2% (17/47), and 33.3% (10/30), respectively (P = 0.02). Nomograms based on stone characteristics, operation duration, and the physical condition of the child were shown to have good discrimination and calibration. The area under the curve of the models was 81% for stone-free rate and 73% for complication rate. The calibration curves showed that the nomogram might underestimate the probability of stone-free rate when the threshold was below 82% and might overestimate the risk of complication rate when the threshold was over 25%. The decision curves demonstrated that the Capital Medical University nomograms improved clinical risk prediction against threshold probabilities of stone-free rate <= 20% and complication rate <= 10%. Conclusions Both the percutaneous nephrolithotomy and flexible ureteroscopy procedures could have acceptable stone-free rates when treating pediatric stones. The Capital Medical University nomograms performed well in helping to predict stone-free and complication rates.