Percutaneous transluminal angioplasty with stenting (PTA/stenting) for intracranial atherosclerotic stenoses is usually performed without any protection devices. We report a unique case of atherothrombotic stenosis with the vulnerable plaque in the cavernous portion of the internal carotid artery (ICA), which was successfully treated by PTA/stenting under cerebral protection with the flow reversal system. A 68-year-old woman presented repetitive transient ischemic attacks in the right ICA territory. Cerebral angiography revealed 80% stenosis in the cavernous portion of the right ICA. High-resolution magnetic resonance imaging (HR-MRI) demonstrated lipid-rich plaques at this lesion. PTA/stenting was performed with a proximal protection device under flow reversal. A filter device captured much amount of atherothrombotic debris with lipid-rich macrophages and leukocytes, which was consistent with HR-MRI findings. Some selected cases of intracranial atherothrombotic ICA stenoses may need endovascular treatment with cerebral protection system. HR-MRI is useful to evaluate plaque characteristics even in the cavernous portion of the ICA.