We report the case of a 25-year-old man with multiple sclerosis (MS) who had severe headache and unconsciousness. He suffered from optic neuritis that had started at age 6. From the age of 12 years, he had suffered from multiple sclerosis (MS) cerebral lesions that relapsed three times over for 5 years. At age 25, he showed a new lesion in the cerebellar cortex, suggesting an exacerbation of the MS. However, magnetic resonance imaging findings the next day showed cerebral venous sinus thrombosis. His laboratory findings showed low antithrombin activity. Genetic analysis revealed a single-base substitution (C>T) at the codon 359 (Arg to STOP) in the 5th exon portion of the antithrombin gene, heterozygote. In the literature review, 17 cases of multiple sclerosis associated with cerebral venous sinus thrombosis, which occurred after the lumbar puncture and the treatment with high-dose methylpredonisolone in 11 of these cases. In our case, antithrombin deficiency, hyperhomocystinemia, infection, and lumbar puncture were suggested as the risk factors.