We report a case of a 53-year-old man with Behçet’s disease (BD) and paradoxical stroke. This patient suddenly developed sensory aphasia, right oculomotor palsy, nystagmus, and left ataxic hemiparesis. MR images showed fresh embolic infarcts in the midbrain and the left parietotemporal lobe. He presented with uveitis, oral aphthous ulcers and genital ulcers. An electrocardiogram revealed no abnormalities, and a transesophageal echocardiogram disclosed a patent foramen ovale. Since venous involvement is common in BD, we suspected the presence of smaller thrombi probable in this patient. We conclude that embolic stroke is a notable complication of BD with right-to-left shunting.