We retrospectively compared anticoagulation with heparin and bivalirudin for 32 consecutive children under 18 years old during extracorporeal membrane oxygenation (ECMO) in our pediatric cardiac intensive care unit (PCICU). Between September 2015 and January 2018, 14 patients received heparin, 13 venoarterial (VA), and 1 venovenous (VV). From February 2018 to September 2019, 18 received bivalirudin (all VA). The mean (standard deviation [SD]) percentage of time with therapeutic activated partial thromboplastin time and activated clotting time was bivalirudin 54 (14%) and heparin 57 (11%), p = 0.4647, and percentage of time supratherapeutic was bivalirudin 18 (10%) and heparin 27 (12%), p = 0.0238. Phlebotomy-associated blood loss per hour of ECMO was double in the heparin compared with bivalirudin group 1.08 ml/h (0.20 ml/h), compared with 0.51 ml/h (0.07 ml/h), p = 0.0003, as well as interventions to control bleeding. Packed red blood cell (PRBC) transfusions significantly correlated with higher blood loss in the heparin group (Pearson correlation coefficient = 0.49, p = 0.0047). Overall amount of blood product utilization was not different between the groups. Survival to ECMO decannulation was 89% for bivalirudin and 57% for heparin, p = 0.0396, although 6 month survival was not significantly different (67% versus 57%, p = 0.5809). Heparin may increase the need for PRBC transfusions and strategies to attenuate bleeding when compared with bivalirudin for children receiving ECMO in PCICU.