To explore the risk factors, prevention, and management of the septic shock following the mini-percutaneous nephrolithotripsy (mini-PCNL). A total of 834 consecutive patients who underwent mini-PCNL from June 2004 to April 2012 were retrospectively analyzed. The causes, prevention, and treatment of septic shock following mini-PCNL were assessed. Twenty out of 834 patients developed septic shock, and 17 patients recovered without complications. Three patients progressed to multiple organ dysfunction syndromes and expired. Multivariable analysis showed that the following variables were independently related to septic shock following mini-PCNL: female, with an odds ratio (OR=1.055E8, P<0.001) and diabetes mellitus (OR=4.192, P=0.001). Female and diabetes mellitus are the risk factors for septic shock following mini-PCNL. Perioperative preventive measures can reduce the incidence of septic shock. Early recognition and timely bundle treatment may decrease the mortality.