Stent thrombosis has been recognized as a potentially critical complication in percutaneous coronary intervention. In the bare-metal stent era, stent thrombosis was considered to be an acute or subacute event, occurring within 1 month after stent implantation. Recently, late or very late stent thrombosis after drug-eluting stent implantation has been brought into focus; however, the mechanism underlying this potentially fatal event is largely unknown. We report a case of critical late thrombosis 2 years after sirolimus-eluting stent implantation. Detailed serial intravascular ultrasound analyses revealed that late-acquired incomplete stent apposition, accompanied by extensive positive vascular remodeling, was involved in the pathogenesis of the nearly fatal event described in this case.