Previous studies of necrotizing enterocolitis (NEC) among infants with hypoplastic left heart syndrome (HLHS) were conducted in single centers or had small sample sizes. This study aimed to determine the mortality rate and the risk factors for NEC among infants with HLHS who were discharged over a 10-year period (2004–2013) from 41 Pediatric Health Information System affiliated children’s hospitals. Either stage 1 palliation and/or heart transplant were completed prior to patient’s death or hospital discharge. We compared the characteristics of infants with HLHS who did not develop NEC and those who developed medical or surgical NEC and of patients who had medical vs. surgical NEC. The primary outcome was mortality over time and by birth weight category (low birth weight [LBW], birth weight < 2500 vs. ≥ 2500 g). Multivariable analyses were performed to identify the risk factors for developing NEC and for mortality among infants with HLHS. The study evaluated 5720 infants with HLHS including 349 patients (6.1%) with medical or surgical NEC. Fifty-two patients (0.9%) required laparotomy or percutaneous abdominal drainage. On univariable analysis, the overall mortality rate for infants who developed NEC was significantly higher than infants who did not develop NEC (23.5 vs. 13.9%, P < 0.001). On multivariable analysis, neither medical nor surgical NEC was a significant predictor of mortality in the study population. LBW infants were at higher risk for mortality in both the univariable and the multivariable models. Nevertheless, LBW did not significantly predispose infants with HLHS to develop NEC. Our results provide a national benchmark incidence of NEC, its risk factors, and outcomes among a large cohort of infants with HLHS and establish that NEC is not a significant risk factor for mortality in this population.