This study aimed to determine the factors that may affect the development of mortality in patients with stage 3b necrotizing enterocolitis (NEC). Between January 2005 and December 2012, patients with the diagnosis of stage 3b NEC who were surgically treated were enrolled in the study. Gestational age, birth weight, presence of hypoxemia history, major congenital heart diseases, enteral feeding, age at perforation, drainage type, operation, and laboratory findings were considered regarding their possible relationship with mortality. Thirty-one patients were enrolled in this study. Following treatment, 15 patients died, while 16 patients recovered and were discharged. Feeding type, high levels of prothrombin time (PT), activated partial thromboplastin time (aPTT), creatinine, and low platelet count, as well as need of inotropic support were associated with mortality. When the cut-off point of platelet level for mortality development in stage 3b NEC was calculated by receiver operating characteristic (ROC) curve, the cut-off point for thrombocyte level was found to be 110,000/µL, with 93.3% sensitivity and 87.5% specificity. Despite the innovations in newborn intensive care, the mortality rate of stage 3b NEC remains very high. Breastfeeding has a significantly positive impact on the survival of patients with NEC. Thrombocytopenia is the most important risk factor of mortality in stage 3b NEC.