Heparin doses are typically maintained at 180–200 s as activated clotting time (ACT) to assess anticoagulant therapy for venous arterial extracorporeal membrane oxygenation (V-A ECMO) in children. However, it is challenging to control the proper heparin dose during V-A ECMO with ACT clinically, which could result in fatal hemorrhagic complications such as cerebral hemorrhage. Although Viscoelastic hemostatic assay (VHA) device: TEG^® 6s (Haemonetics Corp., Boston, USA) could be employed to determine the proper heparin dose during adult ECMO, there is no report about whether TEG^® 6s could be effective for control of heparin therapy during ECMO in children. In our report, we discussed the clinical use of TEG^® 6s for control of heparin therapy during ECMO in children. A 6-month-old female infant with a weight of 6.6 kg was scheduled to undergo an operation for supravalvular and coronary artery stenosis. Because heart failure worsened rapidly, V-A ECMO was needed for circulatory support. We observed that ACT and TEG^® 6s revealed conflicting findings of heparin dose during ECMO. On the second hospital day, ACT was 130–150 s, which requested an increase in heparin. However, TEG^® 6s demonstrated that the CK R-CKH R value was above the upper limit of measurement, which showed excessive heparin dose. We decided that heparin dose was reduced on the basis of TEG^® 6s values. Eventually, V-A ECMO could have been used for 10 days without thrombotic, including intra-circuit thrombus and bleeding complications. Our report revealed the possibility that TEG^® 6s might be better device to decide the proper heparin dose during ECMO in children than the ACT.