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Heparin-induced thrombocytopenia thrombosis (HITT) is a rare and potentially life-threatening complication after abdominal surgery, and it always occurs after the prophylactic or therapeutic use of heparin. HITT after pancreaticoduodenectomy (PD) has not been reported before. Herein, we reported a case of HITT after PD without prophylactic or therapeutic use of heparin. A 74-year-old female patient who suffered resectable pancreatic head cancer was transferred to our center for surgery. An open PD procedure was performed, and the operation was smooth. No heparin was used after surgery. Nine days after surgery, the platelet sharply declined to 48 × 109/L (100–350), and the D-dimer soared up to 33.56 mg/L (0–0.55). Ultrasound examination showed vein thrombosis in both the lower limb and the right upper limb. HIT-antibody was 6.3 U/mL (0–0.6). The diagnosis of HITT was confirmed. Fondaparinux was used. On postoperative day (POD) 23, the platelet recovered to the normal range. On POD 27, she was discharged without thromboembolism or active bleeding, and oral rivaroxaban was prescribed. One month after discharge, the platelet remained normal, and she did not complain of discomfort.