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Background: Acute kidney injury (AKI) is a common complication of hematopoietic stem cell transplantation (HSCT) with increased mortality and morbidity. Understanding the risk factors for AKI is essential. This study aimed to identify AKI incidence, risk factors, and prognosis in pediatric patients post-HSCT. Methods: We conducted a retrospective case–control study of 278 patients who were divided into two groups: those with AKI and those without AKI (non-AKI). The groups were compared based on the characteristics and clinical symptoms of patients, as well as post-HSCT complications and the use of nephrotoxic drugs. Logistic regression analysis was employed to identify the risk factors for AKI. Results: A total of 16.9% of patients had AKI, with 8.5% requiring kidney replacement therapy. Older age (OR 1.129, 95% CI 1.061–1.200, p < 0.001), sinusoidal obstruction syndrome (OR 2.562, 95% CI 1.216–5.398, p = 0.011), hemorrhagic cystitis (OR 2.703, 95% CI 1.178–6.199, p = 0.016), and nephrotoxic drugs, including calcineurin inhibitors, amikacin, and vancomycin (OR 17.250, 95% CI 2.329–127.742, p < 0.001), were identified as significant independent risk factors for AKI following HSCT. Mortality rate and mortality due to AKI were higher in stage 3 patients than those in stage 1 and 2 AKI (p = 0.019, p = 0.007, respectively). Chronic kidney disease developed in 1 patient (0.4%), who was in stage 1 AKI (2.1%). Conclusions: AKI poses a serious threat to children post-HSCT, leading to alarming rates of mortality and morbidity. To enhance outcomes and mitigate these risks, it is vital to identify AKI risk factors, adopt early preventive strategies, and closely monitor this patient group. [ABSTRACT FROM AUTHOR]