The aim of this study was to compare the effects of one-step percutaneous nephrolithotomy (PCNL) by the urologist alone and two-step PCNL by cooperating with the radiologist. We included 168 patients who underwent surgery by the same surgeon, 83 who underwent two-step PCNL, in which percutaneous nephrostomy insertion was performed by the radiologists on the day before endo-surgery, and 85 who underwent one-step PCNL, which involved the creation of a nephrostomy tract and performing the PCNL at the same time in the operating room, by a urologist. We compared the perioperative and postoperative parameters between these two groups. The result revealed that there were no significant differences between one-step and two-step PCNL in the decreases in haemoglobin level and blood transfusion volume, and the hospital stay was shorter in the one-step PCNL group. In addition, the one-step PCNL group was associated with significantly lower visual analogue score (VAS), which were 2.3, 1.1, and 0.4 on the post-operative days 1, 2, and 3, respectively, compared with 3.2, 1.7, and 1.0 in the two-step PCNL group. The number of parenteral analgesic prescriptions was fewer in the one-step PCNL group (0.8 ± 1.1 amps/vials) than in the two-step PCNL group (4.1 ± 2.4 amps/vials). Furthermore, different stone locations barely affected VAS and analgesic administrations. The results indicate that the one-step PCNL by the urologist alone, compared to two-step PCNL with the radiologist, has better wound pain outcome and shorter hospital stay with comparable successful rate and complication grade.