The aims of this study were (1) to describe the additive risk of performing cardiac surgery in neonates born ≤ 2.0 kg, after accounting for the baseline risks of low birth weight, and (2) to describe the additive risk of being born ≤ 2.0 kg in neonates undergoing cardiac surgery. We used a risk difference analysis in a retrospective cohort, 2006–2016. Neonates born ≤ 2.0 kg undergoing congenital heart surgery during initial postnatal admission were included. Data were standardized alternatingly for birth weight and cardiac surgical risk using national population data to estimate the number of deaths expected had they not required cardiac surgery or were they of normal weight. Of 105 neonates ≤ 2 kg, median birth weight was 1.6 kg (IQR 1.3–1.8 kg). Median gestational age was 33 weeks (IQR 31–35 weeks). Observed operative mortality was 14.3%; 0% for neonates ≤ 1.0 kg (CI 0–33.6%), 20.6% for neonates > 1.0–1.5 kg (CI 8.7–37.9%), and 12.9% for neonates > 1.5–2.0 kg (CI 5.7–23.9%). Among neonates ≤ 2.0 kg not undergoing cardiac surgery, expected mortality was 4.8% (CI 1.6–10.8); cardiac surgery increased the risk of mortality 9.5% (CI 1.7–17.4%). Conversely, the expected risk for normal birth weight neonates undergoing cardiac surgery was 5.7% (CI 2.1–12.0%); low birth weight increased the risk of mortality 8.6% (CI 0.5–16.6%). To continue making advancements in cardiac surgery, we must understand that the rate of mortality observed in normal weight infants is not a realistic target and that, despite advances, the risk attributable to the surgery remains higher among low birth weight patients.