Ebstein’s anomaly is frequently detected before birth, with prenatal detection accounting for the majority of cases in the current population. This study aimed to identify the outcome variables among these infants. The medical records of 59 patients with neonatal Ebstein’s anomaly managed at the Asan Medical Center between January, 2001 and June, 2012 were investigated retrospectively. In 46 cases, the diagnosis was made prenatally. Surgical/interventional procedures were performed for 27 of the analyzed patients. Biventricular repair was successful for 12 patients but not for 9 patients with pulmonary atresia. The median follow-up period was 1.96 years (range 0.0–10.4 years). The overall mortality rate was 23.7 % (14/59). Of the 14 deaths, 5 occurred within several hours after birth. The 1- and 5-year survival rates were 78.6 and 76.3 %, respectively. Univariate analysis identified several variables related to the time to death: fetal distress (p = 0.002), prematurity (p = 0.036), low birth weight (p = 0.003), diameter of the atrial septal defect (p = 0.022), and pulmonary stenosis/atresia (p = 0.001). Neither the Carpentier classification (p = 0.175) nor the Celermajer index (p = 0.958) was a significant variable. According to the multivariate analysis, fetal distress (p = 0.004) and pulmonary atresia/stenosis (p < 0.001) were significant determinants of outcome. In conclusion, fetal distress and pulmonary atresia/stenosis are significant predictors of mortality in the current population of patients with neonatal Ebstein’s anomaly. A close cooperation of associated clinicians is required for an improvement in outcome. To establish a better surgical strategy for patients with Ebstein’s anomaly and pulmonary atresia, studies of larger populations are required.