The objective of this study was to compare the clinical efficacy and safety of microchannel percutaneous nephrolithotripsy (MPCNL) with flexible ureteroscopic lithotripsy (FURL) in the treatment of single upper ureteral stones with a diameter of 1-2cm and high hardness. This study retrospectively analyzed 89 patients diagnosed with a single upper ureteral stone with a 1-2cm diameter and a computed tomography value > 1000 Hounsfield units. A propensity score matching system matched this study with factors to minimize the effect of baseline differences between patients. Ultimately, 29 patients in each of the two groups were successfully matched. The stone-free rate was marginally higher in the MPCNL group than in the FURL group (93.10% vs. 86.21%), although the difference did not reach statistical significance (P = 0.666). Furthermore, the mean operative time in the MPCNL group, although slightly longer than that in the FURL group, did not demonstrate a statistically significant difference (P = 0.833). However, patients in the MPCNL group exhibited a significantly more substantial decrease in hemoglobin than those in the FURL group (P < 0.001) and a substantially more extended postoperative hospital stay (P < 0.001). Regarding perioperative complications, the incidence of moderate pain was higher in the MPCNL group than in the FURL group (P = 0.037). The difference in overall complication rates between the two groups did not reach statistical significance (P = 0.108). MPCNL and FURL are efficacious surgical procedures for treating single upper ureteral stones with a 1-2cm diameter and high hardness.