Infants undergoing congenital heart surgery (CHS) with cardiopulmonary bypass (CPB) are at risk of acute kidney injury (AKI) and fluid overload. We hypothesized that placement of a passive peritoneal drain (PPD) can improve postoperative fluid output in such infants. We analyzed 115 consecutive patients, age birth to 60 days, admitted to the PICU after CHS with CPB between 2012 and 2018. Patients who needed postoperative ECMO were excluded. Linear and logistic regression models compared postoperative fluid balances, diuretics administration, AKI, vasoactive-inotropic scores (VIS), time intubated, and length of stay after adjusting for pre/operative predictors including STAT category, bypass time, age, weight, and open chest status. PPD patients had higher STAT category (p = 0.001), longer CPB times (p = 0.001), and higher VIS on POD 1–3 (p ≤ 0.005 daily). PPD patients also had higher AKI rates (p = 0.01) that did not reach significance in multivariable modeling. There were no postoperative deaths. Postoperative hours of intubation, hospital length of stay, and POD 1–5 fluid intake did not differ between groups. Over POD 1–5, PPD use accounted for 48.8 mL/kg increased fluid output (95% CI [2.2, 95.4], p = 0.043) and 3.41 mg/kg less furosemide administered (95% CI [1.69, 5.14], p < 0.001). No PPD complications were observed. Although PPD placement did not affect end-outcomes, it was used in higher acuity patients. PPD placement is associated with improved fluid output despite lower diuretic administration and may be a useful postoperative fluid management adjunct in some complex CHS patients.