Wegener granulomatosis is a systemic vasculitis that mainly affects the upper and lower respiratory tract and the kidneys. The presence of an ischemic stroke in this disease is very rare. A 40-year-old man, smoker with cavitated lesions in both lungs, and inflammation in the nasal mucosa and vocal cords developed an ischemic stroke in the left middle cerebral artery, with the etiological study showing non-bacterial endocarditis. Non-bacterial endocarditis can appear in patients with Wegener granulomatosis, with this being the first case of this cardioembolism reported in this disease.