Bacterial meningitis is a life-threatening condition and Neisseria meningitidis is a major cause. Cerebrovascular complications can occur. Cerebral venous and sinus thrombosis (CVST) is an uncommon type of these complications, especially in meningococcal meningitis. The initiation of anticoagulant in septic thrombosis is controversial. A 35-year-old man was admitted to a hospital with fever and confusion. The diagnosis of N. meningitidis meningitis was established. Antimicrobial regimen (ceftriaxone) was continued. On the 3rd day, the patient's consciousness was improved; however, according to the patient's headache on day 7, brain imaging was performed which revealed a cerebral thrombosis in transverse and sigmoid sinuses. Although initiation of anticoagulant is controversial in septic thrombosis, the anticoagulant treatment also was started. Control brain magnetic resonance venogram done revealed complete resolution of cerebral CVST after 2 weeks. CVST as a complication of meningococcal meningitis should be considered. Anticoagulant treatment may be considered in the management of septic cerebral thrombosis if there are no contraindications. The use of anticoagulant needs further studies.