Delayed sternal closure (DSC) is a technique used in complex cardiac surgery (CCS) and is associated with an increased risk of surgical site infection (SSI). SSI increases hospital stay and healthcare costs, with an incidence ranging from 1.5% to 34%. To determine the SSI rate and associated risk factors in patients with congenital heart disease (CHD) undergoing CCS with DSC between January 2015 and December 2020, and to compare them with previous results, before the implementation of measures by the Healthcare-Associated Infections Committee (HAIC). A descriptive study was conducted in patients under 18 years of age who required DSC between 2015 and 2020 at the Hospital of Pontifical Catholic University of Chile, meeting the Chilean Ministry of Health’s definition of SSI. SSI rates were compared between the periods 2009–2010 and 2015–2020 using the Poisson rate ratio. A total of 1,471 surgeries were performed, of which 138 (9.38%) required DSC and 6 (4.34%) presented SSI. 67% were males older than 7 days, with one patient premature. 66.7% had extracorporeal circulation (ECC) > 200 min and 83.3% required mechanical ventilation (MV) > 5 days. Several SSI-causing microorganisms were identified. Comparing both studies, a decrease in the prevalence of SSI in DSC was found from 22% to 4.3%, with a rate ratio of 5.16 (95% IC 1.83–16.54, p = 0.001), with no significant differences in the risk factors identified in the initial study (ECC > 200 min and MV > 5 days). The SSI rate was 4.34%, a significant decrease compared to the previous study, attributed to improvements in cardiovascular management and IAAS Committee measures.