Association between early renal replacement therapy and better survival has been reported in adults with postoperative kidney injury, but not in children undergoing cardiac surgery. We conducted a retrospective cohort study of 146 neonates and infants requiring peritoneal dialysis following cardiac surgery in a tertiary referral hospital. A propensity score was used to limit selection bias due to timing of dialysis, and included baseline and intraoperative characteristics, requirement for postoperative extracorporeal membrane oxygenation, and creatinine clearance variation. Inverse probability of treatment weighting resulted in good balance between groups for all baseline and intraoperative variables. After weighting, 30-day and 90-day mortality were compared between the 109 patients placed on dialysis early, within the first day of surgery, and those with delayed dialysis, commencing on the second day of surgery or later, using logistic regression and survival analysis. Mortality was 28.1% at 30 days, and was 36.3% during follow-up. Early dialysis was associated with a 46.7% decrease in the 30-day and a 43.5% decrease in the 90-day mortality rate when compared with delayed dialysis. All other short-term outcome variables were similar. Thus, initiation of peritoneal dialysis on the day of or the first day following surgery was associated with a significant decrease in mortality in neonates and infants with acute kidney injury.