Background: Necrotizing enterocolitis (NEC) is a complication that can affect infants with congenital heart disease (CHD). The objective of this study is to determine whether breast milk, which is associated with decreased incidence of NEC in preterm infants, is protective in infants with CHD. Methods: Retrospective case–control study of infants ≥ 33 weeks gestational age with CHD who underwent cardiac surgery during their admission to the Infant Cardiac Unit from 2008 to 2017. Cases were defined as infants with modified Bell's stage ≥ II NEC. Controls were matched by date of birth, gestational age, and pre- or postcardiac surgery feed initiation. Results: A total of 926 infants with gestational age ≥ 33 weeks and CHD were admitted; 18 cases of NEC were identified and compared with 84 controls. Breast milk intake was higher in controls, but this difference was not statistically significant. Single ventricle (SV) physiology was identified as an independent risk factor for NEC by multivariable analysis. Analysis of infants with SV physiology demonstrated that median age at time of surgery was 9 days (interquartile range [IQR], 7-12) in NEC cases and 5 days (IQR, 4-9) in controls ( P = .02). Conclusions: While this study is inconclusive with regard to feeding composition and risk of NEC in infants with CHD, the trend toward greater intake of breast milk in the control group suggests that breast milk may be protective for these infants. Infants with SV physiology are at high risk for NEC. Earlier time to stage I palliation may be a modifiable risk factor for NEC.