Background Hospital-acquired infections (HAIs) are associated with morbidity and mortality in children following congenital cardiac surgery. Our center performs approximately 200 congenital surgeries a year, but infection rates and risk factors remain unknown. This study aims to identify HAI prevalence, risk factors, and outcomes.Methods Retrospective cross-sectional study of children who underwent congenital cardiac surgery between 2018 and 2022. The infection risk factors were identified using univariate and multivariate analyses. Assessed outcomes are length of stay, duration of mechanical ventilation, and mortality.Results Out of 653 patients, 102 (15.6%) developed an infection. Independent risk factors for infection included preoperative critical care admission (odds ratio [OR], 2.7; 95% confidence interval [CI], 1.01-7), delayed sternal closure (OR, 3.3; 95% CI, 1.37-8.0), peritoneal drain (OR, 12.7; 95% CI, 1.65-97), heterotaxy syndrome (OR, 5.6; 95% CI, 1-31), and extracorporeal membrane oxygenation (ECMO) placement in the critical care unit (OR, 10.6; 95% CI, 1.8-64.2). The pediatric critical care and hospital stays of patients with infections were significantly longer with 12.79 (12.15) days versus 4.07(5.47) days and 25.53 (16.86) days versus 10.21 (7.5) days, respectively. Infected patients had a longer mechanical ventilation duration, 169.5 (264.8) versus 28.16 (53.6) hours. Infections were associated with a higher mortality rate, with 7 (6.9%) versus 12 (2.2%).Conclusions The prevalence of HAIs following cardiac surgery was 15.6%. Preoperative critical care unit admission, delayed sternal closure, heterotaxy syndrome, peritoneal drain, and ECMO placement in the critical care unit were independent risk factors. Infected patients have worse outcomes. Preventive strategies are greatly needed.