A 33‐year‐old woman developed deep venous thrombosis at 7 gestational weeks (GW). Heparin‐induced thrombocytopenia was evident at 9 GW during unfractionated heparin infusion. Immediately, anticoagulation therapies together with antithrombin (AT) infusion were commenced with the use of argatroban from 9 GW, and fondaparinux was substituted for argatroban after 24 GW. The patient had hereditary AT deficiency type I determined by laboratory findings and results of genomic DNA analysis. The pregnancy ended in full‐term vaginal delivery of a healthy male without adverse effects of the anticoagulation therapies. This was the first report of a pregnant woman who developed heparin‐induced thrombocytopenia caused by heparin therapy for deep venous thrombosis due to AT deficiency.