Coagulation dysfunction is a serious issue in patients with Coronavirus disease-19 (COVID-19). With regard to recently published studies, a high number of patients with acute respiratory distress syndrome (ARDS) secondary to COVID-19 developed life-threatening thrombotic complications despite anticoagulation. We report a case of young woman with the type-II heparin-binding site (HBS) antithrombin (AT) deficiency (Budapest 3-homozygous), who developed acute deep vein thrombosis on two occasions due to COVID-19 infection in the course of stable anticoagulation with vitamin K antagonist. The first thrombotic event was observed during mild COVID-19 infection, while the second thrombotic event she developed 2 months after she was negative for severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2). Our case highlights the complexity of the treatment in this particular type of thrombophilia and the need for precaution even in mild forms of viral infection. In the treatment of acute thrombosis, AT-deficient patients may benefit from the use of AT concentrate along with low-molecular weight heparin (LMWH), while in cases of type II-HBS, AT supplementation is mandatory.