Adult congenital heart disease (ACHD) patients often require repeat cardiothoracic surgery, which may result in significant morbidity and mortality. Currently, there are few pre-operative risk assessment tools available. In the general adult population, pre-operative cardiopulmonary exercise testing (CPET) has a predictive value for post-operative morbidity and mortality following major non-cardiac surgery. The utility of CPET for risk assessment in ACHD patients requiring cardiothoracic surgery has not been evaluated. Retrospective chart review was conducted on 75 ACHD patients who underwent CPET less than 12 months prior to major cardiothoracic surgery at Children’s Hospital of Wisconsin. Minimally invasive procedures, cardiomyopathy, acquired heart disease, single ventricle physiology, and heart transplant patients were excluded. Demographic information, CPET results, and peri-operative surgical data were collected. The study population was 56% male with a median age of 25 years (17–58). Prolonged post-operative length of stay correlated with increased ventilatory efficiency slope (V_E/\({V_{{\text{C}}{{\text{O}}_2}}}\) slope) (P = 0.007). Prolonged intubation time correlated with decreased peak HR (P = 0.008), decreased exercise time (P = 0.002), decreased heart rate response (P = 0.008) and decreased relative peak oxygen consumption (P = 0.034). Post-operative complications were documented in 59% of patients. While trends were noted between post-operative complications and some measurements of exercise capacity, none met statistical significance. Future studies may further define the relationship between exercise capacity and post-operative morbidity in ACHD patients.