Anticoagulation is essential during extracorporeal membrane oxygenation (ECMO) to prevent catastrophic circuit clotting. Several assays exist to monitor unfractionated heparin (UFH), the most commonly used anticoagulant during ECMO, but no single test or combination of tests has consistently been proven to be superior. This retrospective observational study examines the correlation among antifactor Xa level, activated partial thromboplastin time (aPTT), and UFH dose and the association between antifactor Xa level and aPTT with survival and hemorrhagic and thrombotic complications. Sixty-nine consecutive neonatal and pediatric ECMO patients from September 2012 to December 2014 at a single institution were included. Spearman rank correlation was used to compare antifactor Xa level, aPTT, and UFH dose. Significant but poor correlation exists between antifactor Xa level and UFH dose ρ = 0.1 (p < 0.0001) and aPTT and UFH dose ρ = 0.26 (p < 0.0001). Antifactor Xa level and aPTT were weakly correlated to each other ρ = 0.38 (p < 0.0001). In an univariate analysis, there was no difference between survival and antifactor Xa level, aPTT, or UFH dose. Multiple anticoagulation tests may be superior to a single test during ECMO.