To compare the outcomes of flexible ureterorenoscopy (F-URS) and mini-percutaneous nephrolithotomy (mini-PNL) in the treatment of lower calyceal stones smaller than 2cm. Patients who underwent F-URS and mini-PNL for the treatment of lower calyceal stones smaller than 2cm between March 2009 and December 2014 were retrospectively evaluated. Ninety-four patients were divided into two groups by treatment modality: F-URS (Group 1: 63 patients) and mini-PNL (Group 2: 31 patients). All patients were preoperatively diagnosed with intravenous pyelography or computed tomography. Success rates for F-URS and mini-PNL at postoperative first month were 85.7% and 90.3%, respectively. Operation time, fluoroscopy time, and hospitalization time for F-URS and mini-PNL patients were 44.40min, 2.9min, 22.4h, and 91.9min, 6.4min, and 63.8h, respectively. All three parameters were significantly shorter among the F-URS group (p<0.001). Postoperative hemoglobin drop was significantly lower in F-URS group compared tomini-PNL group (0.39mg/dL vs. 1.15mg/dL, p=0.001). A comparison of complications according to the Clavien classification demonstrated significant differences between the groups (p=0.001). More patients in the F-URS groups require antibiotics due to urinary tract infection, and more patients in themini-PNL group required ureteral double J catheter insertion under general anesthesia. Although both F-URS andmini-PNL have similar success rates for the treatment of lower calyceal stones, F-URS appears to be more favorable due to shorter fluoroscopy and hospitalization times; and lower hemoglobin drops. Multicenter and studies using higher patient volumes are needed to confirm these findings.