Vascular endothelial damage may activate hypercoagulation and contribute to the development of acute kidney injury (AKI). This study aimed to investigate whether early alteration in coagulation was associated with AKI onset following surgeries involving cardiopulmonary bypass (CPB) in children. This single-center retrospective cohort study included 154 infants and toddlers who underwent cardiovascular surgery with CPB. At admission to the pediatric intensive care unit, the absolute thrombin–antithrombin complex (TAT) level in each patient was measured. Moreover, the presence or absence of AKI onset in the early postoperative period was observed. Of the total participants, 55 (35%) developed AKI. A comparison within the toddler group based on the TAT cut-off value showed that both univariate and multivariable associations were found between increased absolute TAT level and AKI onset (odds ratio, 4.70; 95% confidence interval [1.20-17.90]; P = .023). The increase in absolute TAT level in toddlers during the early postoperative period following CPB was associated with AKI onset. However, a further prospective multicenter study with a larger sample size is required for validating these findings.