Coronary artery aneurysm is a serious complication of Kawasaki disease (KD). A 3-month-old infant presented with severe KD 27 days after onset of fever. The patient presented with shock, inferolateral ischemia on electrocardiogram and high troponin. Echocardiography showed severe myocardial dysfunction with diffuse coronary dilation and right coronary artery aneurysm. Arterial Doppler demonstrated thrombosis of aneurysmal axillary and iliac arteries. Withdrawal of support was implemented due to multi-organ failure. Post-mortem optical coherence tomography correlated with pathology. The pulmonary artery was normal on OCT and histology. Coronary arteries showed aneurysmal dilatation, with intimal hyperplasia and preserved media on OCT. Pathology confirmed these findings, with destruction of the internal elastic lamina, luminal myofibroblastic proliferation, neovascularization, and partial disappearance of the media. This is the first report of pathologic correlation in KD with OCT at the subacute stage, which adequately identified structural wall changes.