Children with complex chronic conditions (CCCs) require a disproportionate amount of inpatient resources and are at increased risk of mortality during hospital admissions. This study examines the impact of non-cardiac, comorbid complex chronic conditions on outcomes in children undergoing congenital heart surgery. All admissions associated with a congenital cardiac surgical procedure in the Kids’ Inpatient Database from 1997 to 2012 were examined. Children were classified by the number as well as type (genetic vs. non-genetic) of CCC. Baseline demographics as well as proportion of total inpatient days and total hospitalization charges was assessed. Multivariate regression models examining occurrence of a complication, mortality, prolonged length of stay and high hospitalization charges were constructed. In multivariate models, an increasing number of CCC was associated with increased risk of mortality and complications (mortality: 1 CCC: odds ratio (OR) = 1.17, 95 % CI = 1.03–1.33); ≥2 CCC: OR = 1.54, 95 % CI = 1.26–1.87). Additionally, the presence of a genetic CCC was protective against mortality (OR = 0.71, 95 % CI = 0.56–0.89) while non-genetic CCCs were associated with mortality (OR = 1.62, 95 % CI = 1.41–1.88) and high resource utilization. Over time, the proportion of genetic CCC remained stable while non-genetic CCC increased in prevalence. Complex chronic conditions have a varying association with mortality, morbidity and resource utilization in children undergoing congenital heart surgery. While genetic CCCs were not associated with poor outcomes, non-genetic CCCs were risk factors for morbidity and mortality. These findings suggest that pre-surgical counseling and surgical planning should account for the type of non-cardiac comorbid conditions.