<b><i>Background:</i></b> Congenital diaphragmatic hernia (CDH) often presents with severe cardio-respiratory impairment in the neonatal period. Affected infants may be exposed to multiple nephrotoxic insults, predisposing them to acute kidney injury (AKI). The prevalence of AKI in a CDH cohort has not previously been described. <b><i>Objectives:</i></b> The primary aim of this study was to quantify the prevalence of AKI in patients with CDH treated in a single national centre. Secondarily, we investigated the association between AKI, select neonatal outcomes, and recognised AKI risk factors. <b><i>Methods:</i></b> This was a retrospective analysis of all patients with CDH treated at our regional neonatal surgical centre between September 2011 and December 2017. Data was collected on demographics, CDH Study Group stage (size), laboratory and physiological parameters, medications, mortality, and duration of hospitalisation. AKI severity was stratified using the modified paediatric RIFLE criteria, determined by comparing the percentage increase in serum creatinine from baseline. Statistical analysis was performed using Fisher’s exact and Pearson’s χ² tests for parametric analysis and Mann-Whitney U testing for non-parametric analysis. <b><i>Results:</i></b> Fifty-four CDH patients met the inclusion criteria, 37% of whom developed AKI. The development of AKI was significantly associated with larger CDH defect (type C/D; <i>p</i> = 0.014), extracorporeal membranous oxygenation support (<i>p</i> = 0.003), patch repair (<i>p</i> = 0.004), and exposure to vancomycin, corticosteroids and diuretics (<i>p</i> = 0.004, <i>p</i> = 0.007, and <i>p</i> ≤ 0.001, respectively). There was no statistical association between AKI and gentamicin administration, umbilical arterial catheter insertion, or significant infection. Prolonged hospitalisation and patient mortality were significantly associated with AKI (<i>p</i> = 0.01 and <i>p</i> = 0.001, respectively). <b><i>Conclusions:</i></b> AKI is common in CDH cases treated in our centre and is associated with adverse outcomes. Potentially modifiable risk factors include nephrotoxic medication exposure. Prevention and early recognition of contributory factors for AKI may improve outcomes in CDH.