This study states that Anticoagulation plays a key role in the management of children supported with extracorporeal membrane oxygenation. However, the ideal strategy for monitoring anticoagulation remains unclear. Our objective was to evaluate the utility of laboratory measures of anticoagulation in pediatric extracorporeal membrane oxygenation. Demographic data, laboratory values, and heparin doses were extracted from the enterprise data warehouse. Primary diagnoses, indications for cannulation, hemorrhagic and thrombotic complications, and survival outcomes were abstracted from the local registry used for Extracorporeal Life Support Organization reporting. Statistical models accounting for repeated measures using generalized estimating equations were constructed to evaluate correlations between heparin doses and laboratory values; among laboratory values, and between heparin dose or laboratory values and clinical outcomes. One hundred thirty-three unique patients—78 neonates and 55 older patients—were included in the study. There was no significant association between anti-factor Xa level, activated partial thromboplastin time, activated clotting time, or heparin dose with hemorrhage or thrombosis (odds ratio ≅ 1 for all associations). There was a weak-to-moderate correlation between anti-factor Xa, activated partial thromboplastin time, and activated clotting time in both neonates and older pediatric patients.