ABSTRACT Introduction A randomized trial was conducted prospectively to evaluate the efficacy, related complications, and convalescence of emergency percutaneous nephrolithotomy compared to percutaneous nephrostomy for decompression of the collecting system in cases of sepsis associated with large uretero-pelvic junction stone impaction. Materials and Methods The inclusion criteria included a WBC count of 10.000/mm3 or more and/or a temperature of 38°C or higher. Besides, all enrolled patients should maintain stable hemodynamic status and proper organ perfusions. A total of 113 patients with large, obstructive uretero-pelvic junction stones and clinical signs of sepsis completed the study protocol. Of those, 56 patients were placed in the emergency percutaneous nephrostomy group, while the other 57 patients were part of the percutaneous nephrolithotomy group. The primary end point was the time until normalization of white blood cells (WBC) at a count of 10.000/mm3 or less, and a temperature of 37.4°C or lower. The secondary end points included the comparison of analgesic consumption, length of stay, and related complications. Statistical analysis was performed using SPSS® version 14.0.1. The Mann-Whitney U test, chi-square test, and Fisher’s exact test were used as appropriate. Results The length of hospital stays (in days) was 10.09±3.43 for the emergency percutaneous nephrostomy group and 8.18±2.72 for the percutaneous nephrolithotomy group. This set of data noted a significant difference between groups. There was no difference between groups in regard to white blood cell count (in mm3), time to normalization of white blood cell count (in days), body temperature (in ºC), time to normalization of body temperature (in days), C-reactive proteins (in mg/dL), time taken for C-reactive proteins to decrease over 25% (in days), procalcitonin (in ng/mL), or complication rates. Conclusions This study confirms that emergency percutaneous nephrolithotomy may be as safe as early percutaneous nephrolithotomy in a selected low risk patients with sepsis-associated large, obstructive stone.