The aim of this study is to compare the outcomes of flexible ureteroscopy (fURS) and minimally invasive percutaneous nephrolithotomy (mPNL) for the treatment of renal and/or proximal ureteral stones sized 1-2 cm in the elderly (>= 60 years). Between January 2010 and March 2015, 184 consecutive mPNL and fURS were performed to treat intermediate renal and/or proximal ureteral stones in geriatric patients. The records were retrospectively reviewed and outcomes were compared. Although no significant difference was found in the complication rate between two groups, a statistical trend (p = 0.059) in favor of fURS was observed. In addition, multivariate analysis demonstrated that mPNL, preoperative positive urine culture and lower hemoglobin were independent risk factors for postoperative complication (p = 0.016, p = 0.021, p = 0.001, respectively). And fURS was significantly associated with less hemoglobin drop, red blood cell transfusion, analgesics requirement, postoperative hospital duration, and charges of laboratory tests, medical examinations and medications (p = 0.019, p = 0.037, p = 0.006, p = 0.000 and p = 0.007, p = 0.000, p = 0.000, p = 0.001, respectively), while higher costs of operations (p = 0.008). Receiver operating characteristic curve suggested a preoperative hemoglobin of 106.5 g/L as the threshold for predicting red blood cell transfusion after mPNL. The overall one-session stone-free rate of fURS at 1 month was lower (p = 0.006), while it was similar for solitary stone between two groups. Comorbidity and previous stone surgery did not affect postoperative complication and stone-free rate. This study shows that mPNL is more effective for multiple stones, but fURS is associated with potentially less complications and postoperative hospital stay. Furthermore, preoperative hemoglobin level and urine culture can be used to predict postoperative complication risk and they may be helpful in choosing treatment methods for the elderly.