Few reports have described the prognostic value of measuring both B-type natriuretic peptides (BNP) and high-sensitivity troponin T (hs-TnT) in pediatric patients with complex congenital heart disease (CHD) undergoing surgery. We assessed demographic, hemodynamic, and laboratory data, including BNP and hs-TnT levels, for the prediction of cardiac adverse events in 85 patients. Cardiac adverse events were defined as death, cardiac arrest, worsening heart failure requiring inotropic agents and/or respiratory support, and unscheduled surgery/intervention either within or after 12 months of surgery. There were 17 cardiac adverse events. Of the demographic variables, low birth weight (< 2500 g: Odds ratio [OR], 5.97; 95% confidential interval [CI] 1.48–24.0; p = 0.001) and Ross/New York Heart Association [NYHA] class (≥ 2.0) (OR 12.7; 95% CI 3.08–52.7; p = 0.0004) were strongly association with cardiac adverse events. Among hemodynamic and laboratory variables, preoperative BNP (OR 14.04; 95% CI 2.15–91.7; p = 0.001) and hs-TnT levels (OR 16.66; 95% CI 2.27–122; p = 0.002) were found to be independent risk factors. Receiver operating characteristic analysis determined BNP and hs-TnT levels of 60.9 pg/mL and 0.025 ng/mL, respectively, to be markers of high risk. Kaplan–Meier analysis demonstrated significant differences in the freedom from cardiac adverse events between Group A (BNP or hs-TnT elevated, n = 26) and Group B (both biomarkers elevated, n = 19; log-rank, p < 0.001). In conclusion, low birth weight (< 2500 g) and Ross/NYHA class ≥ 2.0 are strongly associated with cardiac adverse events. Preoperative BNP and hs-TnT also provide prognostic information in patients with complex CHD scheduled for surgery. Using both markers in combination predicts cardiac adverse events better than using either separately.