Background: To evaluate post-operative outcomes and white matter injury (WMI) using brain MRI at term equivalent in neonates with and without severe acute kidney injury (AKI) following surgical necrotizing enterocolitis (NEC). Methods: A retrospective cohort study comparing neonates with severe (Stage 2/3) vs. other (no AKI/Stage 1) AKI using KDIGO classification with multivariable models assessing this association in the context of multiple systemic comorbidities. Results: Of 103 neonates with surgical NEC, 60 (58%) had severe AKI. Those with severe AKI had lower birth weight (BW; 715 vs. 950 g; p =.023), more frequently treated with indomethacin (18.3 vs. 2.4%); p =.014), higher CRP levels at 24 h after NEC onset (14.4 [6.4–19.8] vs. 4.8 [1.6–13.4]; p =.005), higher presence of cholestasis (73.3 vs. 51.2%); p =.023), later age of NEC onset (14 vs. 7 d); p =.004), longer length of bowel resected (14.9 vs. 4.3 cm); p =.011), longer post-operative ileus days (14 vs. 9 d); p <.001), longer post-operative days at starting enteral feedings (15 vs. 10 d; p <.001), longer days of attainment of full enteral feedings (75 vs. 44.5 d; p =.008) and longer length of stay (140.5 vs. 94 d; p =.028) compared to those without severe AKI. Compared to infants without AKI by serum creatinine, those with AKI had significantly more cases of white matter abnormality (WMA; 90 vs. 36.6%; p <.001) and retinopathy of prematurity (63.9 vs. 35.3%; p =.017). In addition, the presence of AKI Stage 2 and 3 by serum creatinine was independently associated with higher odds of sustaining severe WMI level on an ordinal scale (OR = 6.2; 95% CI = (1.1–35.5); p =.041). Conclusions: Neonates with severe AKI following surgical NEC were more likely to experience longer post-operative morbidity and higher WMI by MRI at term.