Congenital heart disease (CHD) is often associated with chronic extracardiac co-morbid conditions (ECC). The presence of ECC has been associated with greater resource utilization during the operative period; however, the impact beyond hospital discharge has not been described. This study sought to understand the scope of chronic ECC in infants with CHD as well as to describe the impact of ECC on resource utilization after discharge from the index cardiac procedure. IRB approved this retrospective study of infants <1 year who had cardiac surgery from 2006 and 2011. Demographics, diagnoses, procedures, STAT score, and ECC were extracted from the medical record. Administrative data provided frequency of clinic and emergency room visits, admissions, cumulative hospital days, and hospital charges for 2 years after discharge from the index procedure. Data were compared using Mann–Whitney Rank Sum Test with p < 0.05 considered significant. ECC occurred in 55% (481/876) of infants. Median STAT score was higher in the group with ECC (3 vs. 2, p < 0.001). Resource utilization after discharge from the index procedure as defined by median hospital charges (78 vs. 10 K, p < 0.001 and unplanned hospital days 4 vs. 0, p < 0.001) was higher in those with ECC, and increased with the greater number of ECC, even after accounting for surgical complexity. STAT score and the presence of multiple ECC were associated with higher resource utilization following the index cardiac surgical procedure. These data may be helpful in deciding which children might benefit from a cardiac complex care program that partners families and providers to improve health and decrease healthcare costs.