Abstract The course of COVID-19 patients may be complicated by thromboembolic events. We report on a 48-year-old female COVID-19 patient who underwent surgical removal of a large intracardiac thrombus. As per our centre protocol, critically ill COVID-19 patients are anticoagulated by the direct thrombin inhibitor Argatroban with close monitoring of anti-IIa activity. An intra-atrial thrombus formation fixed in a patent foramen ovale but also large mobile portions in both atria was diagnosed 4 days after weaning and removal of the jugular and femoral extracorporeal membrane oxygenation cannulas. The thrombus was removed surgically via median sternotomy and on cardiopulmonary bypass. The thrombus had a bizarre appearance with several finger-like appendices, and histological analysis revealed a mixed picture of acute and chronic thrombus portions. This case highlights the risk of life-threatening thrombus formation in COVID-19 patients despite therapeutic thrombin inhibition.