Background: The aim of this study is to evaluate the causal relation between hospital-acquired infection (HAI) and clinical outcomes following cardiac surgery in neonates and infants and to identify the risk factors for the development of HAI in this subset of patients. Materials and Methods: After Ethics committee approval, one hundred consecutive infants undergoing open heart surgery (OHS) between June 2015 and June 2016 were included in this prospective observational study. Data were prospectively collected. The incidence and distribution of HAI, the microorganisms, their antibiotic resistance and patients′ outcome were determined. The Centers for Disease Control and Prevention criteria were used for defining HAIs. Univariate and multivariate risk factor analysis was done using Stata 14. Results: Sixteen infants developed microbiologically documented HAI after cardiac surgery. Neonatal age group was found to be most susceptible. Lower respiratory tract infections accounted for majority of the infections (47.4%) followed by bloodstream infection (31.6%), urinary tract infection (10.5%), and surgical site infection (10.5%). Klebsiella (36.8%) and Acinetobacter (26.3%) were the most frequently isolated pathogens. HAI was associated with prolonged ventilation duration (P = 0.005), Intensive Care Unit stay (P = 0.0004), and hospital stay (P = 0.002). Multivariate risk factor analysis revealed that preoperative hospital stay (odds ratio [OR] 1.22, 95% confidence interval (CI) 1.6-1.39, P = 0.004), and prolonged cardiopulmonary bypass (CPB) (OR 1.03, 95% CI 1.01-1.05, P = 0.001) were associated with the development of HAI. Conclusion: HAI still remains a dreaded complication in infants after OHS and contributing to morbidity and mortality. Strategies such as decreasing preoperative hospital stay, CPB time, and early extubation should be encouraged to prevent HAI.