Anticoagulation is mandatory during venoarterial extracorporeal membrane oxygenation (V-A ECMO) flow reduction trials with very low blood flow. Anticoagulation in the ECMO circuit might be intensified with less effect in the patient by temporarily increasing the heparin dose directly connected to the oxygenator. We performed a prospective observational study in 16 patients on V-A ECMO, measuring anticoagulation parameters before and at the end of flow reduction trials in both the patients’ circulation and the ECMO circuit, while having increased the heparin infusion rate during the flow reduction trial. The heparin infusion rate was doubled in eight patients for 30 [25–30] minutes, which resulted in an increase in activated partial thromboplastin time (APTT) of 5 seconds [2–6] in the patient and 13 seconds [5–20] in the ECMO circuit (p = 0.03). Heparin was tripled in eight patients for 22 [18–27] minutes, which resulted in an increase in APTT with 5 seconds [3–9] in the patient and 10 seconds [5–22] in the ECMO circuit (p = 0.02). In conclusion, increased APTT levels in the ECMO circuit during flow reduction trials can be achieved by increasing heparin infusion rates via the ECMO circuit, with minor effects in the patient. This can be helpful in patients with high bleeding risk.