Aim: To assess the utility of neutrophil gelatinase-associated lipocalin (NGAL) in both urine and serum as a follow-up marker for the discrimination of prerenal acute kidney injury (AKI) from intrinsic AKI in critically ill pediatric patients with established AKI at the time of patient presentation. Patients and methods: This was a prospective cohort study of a heterogeneous group of critically ill children in the pediatric intensive care unit (PICU). Serum creatinine (SCr) values were obtained daily as part of routine patient care. AKI was defined as a 50% or greater increase in SCr from baseline and classified as prerenal and intrinsic AKI. Results: A total of 32 critically ill children (mean age: 105 ± 71.7 months, 56% female) with established AKI were included to the study. Area under curve (AUC) for urine and serum NGAL to distinguish prerenal AKI from intrinsic AKI was 0.94, 95% confidence interval (CI): 0.869–1.02 (p < 0.001) and 0.86, 95% CI: 0.71–1.02 (p = 0.002), respectively. Conclusion: In a heterogeneous group of critically ill children with established AKI, we found that NGAL in both urine and serum at the time of patient presentation discriminated intrinsic AKI from prerenal AKI.