Background Acute kidney injury (AKI) after cardiac surgery (CS-AKI) in children with congenital heart disease is a serious complication closely associated with high morbidity and mortality. Kidney Disease: Improving Global Outcomes (KDIGO) AKI staging demonstrates high sensitivity for detecting AKI and predicting associated in-hospital mortality. However, neonatal-modified KDIGO criteria (n-KDIGO), recently introduced as a standard diagnostic tool, for CS-AKI have not been fully validated. Here, we evaluated the incidence of risk factors and postoperative outcomes of neonatal CS-AKI. Methods We retrospectively studied 114 consecutive neonates who underwent cardiac surgery at the Kagoshima University Hospital. CS-AKI was classified using the n-KDIGO criteria. Risk adjustment in congenital heart surgery (RACHS-1) score was used to predict the complexity-adjusted mortality and % fluid overload (%FO) was used to monitor fluid balance in pediatric cardiac surgery. Results Among 81 patients, neonatal CS - AKI occurred in 57 (70.4%) patients according to n-KDIGO criteria. Of these, 28 (34.6%) patients reached n-KDIGO 1, 17 (21.0%) reached n-KDIGO 2, and 12 (14.8%) reached n-KDIGO 3. Patients with CS-AKI had significantly higher vasoactive-inotropic score levels, longer operative times, and higher %FO than patients without CS-AKI. Notably, increased duration of cardiopulmonary bypass times and %FO were risk factors for the development of neonatal CS-AKI. The n-KDIGO-based severe AKI grade had higher risk of in-hospital mortality; however, the n-KDIGO-based mild AKI grade was not associated with any postoperative outcomes. Conclusions CS-AKI based on n-KDIGO criteria is common in neonates and is closely associated with higher mortality, especially in patients with severe CS-AKI.