Neonatal cardiac surgery requires careful consideration of cardiopulmonary bypass (CPB) priming fluid composition due to small blood volume and immature physiology. This study investigated the impact of allogeneic stored red blood cells (RBCs) processed using an autotransfusion system in CPB priming fluid for neonates. We compared perioperative parameters, inflammatory mediators, coagulation indicators, vasoactive-inotropic score (VIS) and clinical outcomes between neonates receiving unwashed (n = 56) and washed (n = 45) RBCs in CPB priming fluid. Regression models were used to assess the independent association between RBC washing and patient outcomes. The autotransfusion system improved stored RBC quality. The washed group showed higher peak haematocrit (p < 0.01) and haemoglobin levels (p = 0.04) during CPB, an increased oxygen delivery index during rewarming (p < 0.05) and lower postoperative lactate levels and VIS (p < 0.05). Inflammatory (IL-6, IL-8 and IL-10) and coagulation parameters (D-dimer, fibrinogen and fibrin degradation product) fluctuated compared with baseline but did not significantly differ between groups. The washed group had a lower incidence of hyperlactacidaemia and delayed sternal closure at CPB weaning. Adding washed allogeneic stored RBCs to neonatal CPB priming fluid reduced postoperative lactate elevation and VIS without early improvement in the inflammatory and coagulation systems.