Surgical site infection (SSI) occurs in 0.25% to 6% of children after cardiothoracic surgery (CTS). There are no published data regarding the financial impact of SSI after pediatric CTS. We sought to determine the attributable hospital cost and length of stay associated with SSI in children after CTS. We performed a retrospective, matched cohort study in a 26-bed cardiac intensive care unit (CICU) from January 2010 through December 2013. Cases with SSI were identified retrospectively and individually matched to controls 2:1 by age, gender, Risk Adjustment for Congenital Heart Surgery score, Society of Thoracic Surgeons-European Association for Cardiothoracic Surgery category, and primary cardiac diagnosis and procedure. Of the 981 cases performed during the study period, 12 with SSI were identified. There were no differences in demographics, clinical characteristics, or intraoperative data. Median total hospital costs were higher in participants with SSI as compared to controls (US$219,573 vs US$82,623, P < .01). Children with SSI had longer median CICU length of stay (9 vs 3 days, P < .01), hospital length of stay (18 vs 8.5 days, P < .01), and duration of mechanical ventilation (2 vs 1 day, P < .01) and vasoactive administration (4.5 vs 1 day, P < .01). Children with SSI after CTS have an associated increase in hospital costs of US$136,950/case and hospital length of stay of 9.5 days/case. The economic burden posed by SSI stress the importance of infection control surveillance, exhaustive preventative measures, and identification of modifiable risk factors.