This study sought to determine overall hospital cost in children with congenital heart disease (CHD) and to compare cost associated with cardiac surgical procedures, cardiac catheterizations, non-cardiac surgical procedures, and medical admissions. The 2012 Healthcare Cost and Utilization Project Kid's Inpatient Database was used to evaluate hospital cost in neonates and children with CHD undergoing cardiac surgery, cardiac catheterization, non-cardiac surgical procedures, and medical treatments. Multivariable logistic regression was applied to determine independent predictors for increased hospital cost. In 2012, total hospital cost was 28,900 M$, while hospital cost in children with CHD represented 23% of this total and accounted for only 4.4% of hospital discharges. The median cost was $51,302 ($32,088-$100,058) in children who underwent cardiac surgery, $21,920 ($13,068-$51,609) in children who underwent cardiac catheterization, $4134 ($1771-$10,253) in children who underwent non-cardiac surgery, and $23,062 ($5529-$71,887) in children admitted for medical treatments. Independent predictors for increased cost were hospital bed size <400 beds (P < 0.001), more than four procedures performed during the same hospitalization (P = 0.001), use of ECMO (P < 0.001), length of hospital stay exceeding 14 days (P < 0.001), cardiac failure (P < 0.001), sepsis (P < 0.001), acute kidney injury (P < 0.001), and neurologic (P < 0.001) and thromboembolic complications (P < 0.001). Hospital cost in children with CHD represented 23% of global cost while accounting for only 4.4% of discharges. This study identified factors associated with increased cost of cardiac surgical procedures, cardiac catheterizations, non-cardiac surgical procedures, and medical management in children with CHD.