Surgery in patients with congenital or acquired coagulation defects has always been challenging and requires special care with a multidisciplinary approach. Percutaneous nephrolithotomy (PCNL) is a standard procedure performed in patients with kidney stones. Although prone to bleeding more than most of the widely performed surgical procedures, there are not much data regarding PCNL in patients with bleeding disorders or coagulation defects. There are only case reports or series with a small number of patients for the patients with common coagulation defects, including hemophilias. Moreover, there are no reports about PCNL in rare bleeding disorders. In this study, we reported a case referred for kidney stone treatment and diagnosed as Factor VII deficiency during preoperative evaluation. Because it is one of the rare bleeding disorders, we also reviewed the literature in this field.