Objetives Extracorporeal membrane oxygenation (ECMO) after surgery for congenital heart disease (CHD) provides hemodynamic support to patients when their myocardial function is temporarily affected. Postoperative infections in children with CHD on ECMO are a significant challenge, as they complicate recovery and affect outcomes during this critical period of hemodynamic support. The objective of this study was to analyze the mortality related to the micro-organism isolated in children with ECMO after surgery for CHD. Methods Retrospective cohort study from January 2014 to December 2021 at a university hospital in Colombia. The primary outcome was the infection-related inpatient mortality of children undergoing surgery for CHD who received ECMO support, according to the type of microorganisms isolated in cultures. Results A total of 3307 surgeries for CHD were performed during the study period. Of these, 108 (3.3%) required veno-arterial ECMO after surgery. We found positive cultures in 35% of these patients. The incidence of infection was 14.5 cases per 1000 days of ECMO. The overall mortality of infected patients was 54.1%. Isolation of Gram-negative bacteria in cultures was associated with higher odds of dying compared with other isolations, regardless of age and type of CHD (aOR 6.92 95% CI 1.91-25.02; p < .01). We found no differences in hospital length of stay or PICU stay based on the type of bacteria isolated. The most commonly isolated Gram-negative bacteria was Klebsiella pneumoniae , which was associated with longer mechanical ventilation [26 (IQR 18.2-31.0) versus 11 (IQR 8.0-15.0) days; p < .01]. Conclusions The presence of a Gram-negative bacterium as the cause of infection in any sample was associated with increased odds of mortality in children receiving ECMO support in the postoperative period following corrective surgery for congenital heart disease. Infections occurred in 1 out of 3 children on ECMO following surgery for CHD.