Congenital heart defect (CHD) surgeries are performed with cardiopulmonary bypass (CPB) and are complicated by several factors that affect the child’s brain. However, to date, the number of studies on brain protection in cardiac surgery remains small. The aim of this study was to assess the impact of refraining from using packed red blood cells (PRBCs) in priming solutions in children with congenital defects (CHDs) who require surgical interventions using CPB to prevent brain injury in the postoperative period. Material and methods: This study included 40 children, and the mean age was 14 (12–22.5) months and the mean weight was 8.8 (7.25–11) kg. All patients underwent CHD closure using CPB. The patients were divided into two groups depending on the use of PRBCs in the priming solution. Brain injury was assessed using three specific blood serum markers, namely S100 calcium-binding protein β (S100β), neuron-specific enolase (NSE) and glial fibrillary acidic protein (GFAP) before surgery, after the completion of CPB and 16 h after surgery (first, second and third control points). Markers of systemic inflammatory response were also analyzed, including interleukin-1, -6, -10 and tumor necrosis factor alpha (TNF-α). A clinical assessment of brain injury was carried out using a valid, rapid, observational tool for screening delirium in children of this age group, i.e., “Cornell Assessment of Pediatric Delirium”. Results: Factors of the intra- and postoperative period were analyzed, such as hemoglobin levels, oxygen delivery (cerebral tissue oxygenation, blood lactate level and venous oxygen saturation) and indicators of organ dysfunction (creatinine, urea, bilirubin levels, duration of CPB and length of stay in the ICU). Following the procedure, there were no significant differences between the groups and all indicators were within the reference values, thus demonstrating the safety of CHD closure without transfusion. Moreover, the highest level of specific markers of brain injury were noted immediately after the completion of CPB in both groups. The concentration of all three markers was significantly higher in the group with transfusion after the completion of CPB. Moreover, GFAP levels were higher in the transfusion group and 16 h after surgery. Conclusions: The results of the study show the safety and effectiveness of brain injury prevention strategies that consist of not conducting PRBC transfusion.