Background: Children with congenital heart diseases (CHDs) often require cardiac surgery, whose outcome depends on many preoperative, intraoperative, and postoperative factors. Objectives: We aimed to investigate the factors associated with in-hospital mortality among patients undergoing pediatric heart surgery for CHDs. Methods: This retrospective cross-sectional study included patients younger than 18 who underwent cardiac surgery due to CHDs at the Children's Medical Center of Tehran University of Medical Sciences and were admitted to the open-heart surgery intensive care unit (OH-ICU) between March 2018 and March 2019. Patients with incomplete records were excluded. The collected data included age (months), weight (kg), type of congenital defect, duration of intensive care unit (ICU) stay, cardiopulmonary bypass (CPB) time, aortic cross-clamping (XCT) time, postoperative (day 1) platelet count and neutrophil-to-lymphocyte ratio (NLR), and mortality. Results: This study included 275 CHD patients who underwent cardiac surgery. The mean age and weight were 32.54 ± 37.4 months and 11.01 ± 8.43 kg, respectively. Those who died were younger (P = 0.05) and had lower weights (P = 0.001). An inverse relationship existed between thrombocytopenia and mortality. The NLR was higher in those who survived (mean 4.08 vs. 2.87), while the deceased patients had an extended duration of hospitalization, longer CPB time, and longer XCT time. Conclusions: Younger age, lower body weight, lower NLR ratio, lower platelet count, longer intraoperative CPB time, and XCT time were not associated with increased in-hospital mortality following cardiac surgery for CHDs. The Risk Adjustment for Congenital Heart Surgery (RACHS-1) score was not significantly related to mortality. Also, CPB and XCT times were significantly longer in cyanotic than in non-cyanotic patients. Cyanotic patients also had significantly lower platelets than non-cyanotic patients after the operation. Large, multicenter studies are needed to further investigate the predictors of mortality following surgery for CHDs.