Gastrointestinal bleeding is a potential complication in paediatric patients undergoing cardiopulmonary bypass, as it develops secondary to low gastrointestinal perfusion. This study aimed to examine the incidence of gastrointestinal bleeding and identify its risk factors in these patients. This retrospective study was undertaken to examine the demographic features, clinical findings, and operative data of paediatric patients under years old who had undergone congenital heart surgery with cardiopulmonary bypass between November 1, 2021, and November 1, 2023. The study aimed to investigate the incidence of gastrointestinal bleeding associated with cardiopulmonary bypass and to identify potential risk factors for gastrointestinal bleeding. The obtained results were statistically evaluated. The study period included 1100 patients who underwent congenital heart surgery with cardiopulmonary bypass. Fifty-two percent of the total participants were male. The median weight of the patients was 4.4 kg, with an interquartile range of 3.5-5.8 kg. The patients were categorised by age, revealing that 62% were newborns, 24% were infants, and 14% were children. Forty-four (4.2%) of the total number of patients experienced gastrointestinal bleeding. Newborns had a significantly higher incidence of bleeding (6% or 34 patients) compared to infants (3% or 8 patients) and children (1.5% or 2 patients) (p < 0.05). Patients who experienced gastrointestinal bleeding had a longer median hospital stay of 24 days compared to those who did not, with a median hospital stay of 14 days. Moreover, patients who suffered from bleeding had a significantly higher mortality rate (30%) in comparison to those who did not (9.9%) (p < 0.05). The incidence of gastrointestinal bleeding was found to be associated with several risk factors, such as low operative age and weight, high surgical score, presence of low cardiac output syndrome, extracorporeal membrane oxygenation (ECMO) usage, high lactate levels, and low platelet count. Gastrointestinal bleeding is a potential complication for patients who undergo cardiopulmonary bypass. It is particularly relevant for newborns who have undergone prolonged surgery, have a high surgical complexity score, exhibit high lactate levels, display low cardiac output, utilise ECMO, and possess low platelet counts. In such cases, there may be a heightened incidence of gastrointestinal bleeding. It is important to consider this possibility in order to ensure the best possible patient outcomes.