Background Congenital Heart Disease (CHD) places an enormous economic burden on families of affected children in Nigeria. This study sought to determine the healthcare costs of pre-surgical management of CHD and describe its effects on the family’s income.Methods Using a semi-structured interviewer-administered questionnaire, family income, type of CHD, co-morbidity, healthcare payment mechanism and healthcare cost were investigated among 121 families with CHD children. Indicators of Catastrophic Health Expenditure (CHE); healthcare spending in excess of 10% family income were calculated. Factors associated with increased healthcare spending in CHD management were explored using the Kruskal Wallis test of significance.Results Of the 121 parents interviewed, about 80% paid for healthcare using out-of-pocket payment mechanism. Mean annual total cost of healthcare was ₦87,951± ₦120,213 ($244.31± $333.92) with direct medical care accounting for 81.0% of this total annual cost. Mean annual consultation, medication, investigation and admission cost were ₦5,515 ($15.32), ₦57,882 ($160.78), ₦30,462 ($84.62) and ₦87,789 ($243.86) respectively. Mean estimated annual indirect cost was ₦19,233 ± ₦31,722 ($53.42 ± $88.12). Incidence of CHE was 35.5% while catastrophic overshoot and mean positive overshoot attributable to CHD healthcare cost were 6.5% and 32.9% of family income respectively. Healthcare cost was significantly higher in families of children with co-morbidities (p = 0.016) and those who suffered financial catastrophe (p = 0.001). Health insurance did not significantly reduce healthcare spending among the insured.Conclusion The economic burden of pre-surgical management of children with CHD is high in Nigeria. There is the need to scale up the inclusion of CHD under the National health insurance scheme.