A 69-year-old woman underwent percutaneous coronary intervention for a severe stenotic lesion in the bifurcation of the mid-left anterior descending artery and first diagonal branch. A single stent was implanted into the left anterior descending artery. After the stent strut was dilated by balloon inflation in the diagonal branch, dissection occurred at the ostium of the diagonal branch and resulted in side branch occlusion due to hematoma. Bailout stenting was performed in the diagonal branch, but thrombus projection occurred in the left anterior descending artery. Aspiration, balloon inflation and thrombolytic therapy were performed, but distal embolism developed. This case illustrates that thrombus projection caused by stenting in a side branch may occur as a rare complication in percutaneous coronary intervention.