Background: This study aimed to evaluate the incidence of ventilator-associated pneumonia (VAP) and identify the risk factors contributing to its development in pediatric cardiac intensive care units. Methods: This retrospective study analyzed cases of patients <18 years old hospitalized in a pediatric cardiac intensive care unit between 01 January 2021, and 01 January 2024. Data patients diagnosed with VAP were matched (age and surgical procedure) with those of two control patients based. Results: During the study period, 1650 cardiac operations were performed. Among these, 520 cases requiring mechanical ventilation for more than 48 hours were included in the analysis. A total of 40 cases of VAP were identified and matched with 80 control cases. The incidence density of VAP was found to be 17.2 per 1000 ventilator days, and the median age of patients with VAP was two months. The isolated pathogens included Klebsiella pneumoniae (n = 14, 35%), Stenotrophomonas maltophilia (n = 7, 17.5%), Pseudomonas aeruginosa (n = 6, 15%), Acinetobacter baumannii (n = 6, 15%), Staphylococcus aureus (n = 4, 10%) and Enterobacter species (n = 3, 7.5%). The mortality rate in patients with VAP was 20% (8/40). Data analysis showed that independent risk factors for VAP included a RACHS-1 (Risk Adjustment for Congenital Heart Surgery) score of ≥4, the use of extracorporeal membrane oxygenation (ECMO), central venous catheterization lasting ≥14 days, mechanical ventilation dependency for ≥10 days, requirement for total parenteral nutrition, and delayed sternal closure of ≥2 days. Conclusions: VAP represents a significant cause of morbidity and mortality in pediatric cardiac intensive care units after congenital heart surgery. Gram-negative bacteria were identified as the predominant pathogens in this population.