Objectives <p>This study aimed to evaluate the prognostic significance of serum endocan levels in pediatric patients undergoing congenital heart surgery with cardiopulmonary bypass (CPB).</p> Methods <p>This prospective observational study included 31 patients. Endocan levels were measured preoperatively, and postoperative day 1 and 6. Correlations between endocan levels, laboratory, clinical parameters were analyzed using Spearman’s rank correlation and receiver operating characteristic (ROC) analysis.</p> Results <p>Preoperative endocan levels were higher in patients with adverse outcomes, however it didn’t reach statistical significance. The ROC analysis demonstrated a moderate predictive capacity of preoperative endocan levels for mortality (AUC = 0.68). A statistically significant positive correlation was found between endocan and aspartate aminotransferase (AST) (r = 0.42, <i>p</i> = 0.020), while a significant negative correlation was observed with the neutrophil count (r =  − 0.38, <i>p</i> = 0.034). No significant associations were identified with Aristotle scores or acute kidney injury (AKI). Preoperative endocan levels showed trends toward associations with adverse outcomes but lacked sufficient discriminative power.</p> Discussion <p>Endocan does not appear to be a reliable standalone predictor of postoperative risk. Further studies with larger samples and serial measurements are needed.</p>