Incidence and outcomes of acute kidney injury (AKI) among neonates who underwent open-heart surgery are not well highlighted in the literature. We aim to assess the incidence, risk factors, and outcome of AKI among neonates undergoing open-heart surgery. This is a retrospective cohort study between 2016 and 2021 for all neonates requiring open heart surgery. The cases were divided into 2 groups: the AKI (index) group and the non-AKI (control) group. The two groups were statistically compared for risk factors, needs for dialysis, and outcomes. 100 patients fulfilled the inclusion criteria. Among them, 74 (74%) developed AKI, including 41 (55%), 15 (21%), and 18 (24%) patients in KDIGO stages 1, 2, and 3, respectively. Multivariate analysis comparing both groups demonstrated that low pre-operative creatinine (p = 0.01), prolonged bypass time (p = 0.0004) and high vasoactive inotropic score (VIS), (p = 0.0008) were risk factors for developing AKI post-operatively. Furthermore, in the AKI group, 17 (23%) neonates required renal replacement therapy in the form of peritoneal dialysis. The length of stay was higher in the AKI index group (p = 0.015). Patients who had AKI recovered their kidney function at discharge. There was no difference in mortality between both groups. The AKI occurred in 74% of neonates undergoing open-heart surgery, with 23% of them needing peritoneal dialysis. Low pre-operative creatinine, high VIS score, and prolonged bypass time are potential risk factors for AKI development after neonatal open-heart surgery. AKI may lead to prolonged hospitalization, though most affected patients recovered their normal kidney function at discharge.