Background: During pediatric epilepsy surgery, due to low circulating blood volume, intraoperative bleeding can result in significant hemodynamic instability, thereby requiring meticulous hemodynamic and transfusion strategies. Knowing the source of bleeding during the procedure would allow medical staff to better prepare the perioperative protocols for these patients. We compared intraoperative bleeding between the first (involving skin to meninges) and second (involving brain parenchyma) stages of epilepsy surgery to investigate the differences between various anatomical sites. Methods: We reviewed the electronic medical records of 102 pediatric patients < 14 years old who underwent two-stage epilepsy surgeries during January 2012–2016. Invasive subdural grids were placed via craniotomy during Stage 1 and the epileptogenic zone was removed during Stage 2 of the surgery. We compared the volume of intraoperative bleeding between these two surgeries and identified variables associated with bleeding using multivariate regression analysis. Results: Both surgeries resulted in similar intraoperative bleeding (24 vs. 26 ml/kg, P = 0.835), but Stage 2 required greater volumes of blood transfusion than Stage 1 (18.4 vs. 14.8 ml/kg, P = 0.011). Massive bleeding was associated with patients < 7 years old in Stage 1 and weighing < 18 kg in Stage 2. Conclusions The volume of intraoperative bleeding was similar between the two stages of pediatric epilepsy surgery and was large enough to require blood transfusions. Thus, blood loss during pediatric epilepsy surgery occurred at both anatomic sites. This indicates the necessity of early preparation for blood transfusion in both stages of pediatric epilepsy surgery.