A 30-year-old Japanese man was diagnosed with chronic thromboembolic pulmonary hypertension (CTEPH) with lupus anticoagulants (LAs) in 2003. He underwent pulmonary endarterectomy after the placement of an inferior vena cava filter (IVCF) in 2004, and treatment with warfarin was continued. In 2014, IVCF occlusion and marked collateral circulation were noted during an examination for transient dyspnea; however, his warfarin level was within the therapeutic range for 88.9% of the time from 2003 to 2014. We herein report a rare case of CTEPH and LAs with IVCF occlusion; in such cases, intense treatment may be required.