Factor XI deficiency is a rare inherited coagulopathy first described in Ashkenazi Jews. In Japanese populations, factor XI deficiency is thought to be very rare. This disorder causes unique problems during percutaneous coronary intervention (PCI). During PCI, prevention of thrombosis is important and heparin is usually used for anticoagulation. However, care must also be taken to avoid serious complications of bleeding. These two situations are contradictory and anticoagulation with heparin might increase severe bleeding in patients with factor XI deficiency. An 84-year-old Japanese woman was admitted to our hospital for the treatment of worsening effort angina pectoris. A coronary angiography revealed severe stenotic lesions at the left main trunk (LMT) and the right coronary artery (RCA). While performing PCI of the LMT, 8,000 U of heparin were used and the patient underwent successful drug-eluting stent implantation. At this point, the patient's activated coagulation time was over 1,500 s and there was a marked decrease of factor XI activity (<3%: normal range 75-145%). After the diagnosis of factor XI deficiency, PCI for the RCA was scheduled without anticoagulation and fresh frozen plasma instead of dual antiplatelet therapy by aspirin and clopidogrel. Two drug-eluting stents were deployed and dilation using the kissing balloon technique was performed. The procedure was uneventful without stent thrombosis or distal embolization or bleeding. Because the literature on stenting for patients with factor XI deficiency is very limited, this case provides additional clinical information.