The use of drug-eluting stents (DES) provides early and late benefits demonstrated by angiographic and clinical outcomes. Here we report a case of late stent thrombosis and acute myocardial infarction caused by late stent malapposition (LSM) of a DES at 16 months after the procedure. We successfully treated the patient with balloon angioplasty after intravenous thrombolytic therapy. This case illustrates that a LSM can develop at any time after DES implantation and can result in acute coronary syndrome. Therefore, clinicians should be aware of the possibility of late cardiac events after implantation of DES.