Meningococcal infections are an important cause of mortality and morbidity in childhood. Herein we report a 2-year-old Syrian refugee boy living in Turkey diagnosed with Neisseria meningitidis serotype B infection complicated with intracranial empyema. Refugees are a sensitive population in all aspects especially infectious diseases. Endemic diseases in the refugees' own countries constitute a major health problem. Vaccination in sensitive populations and in the country would be important precaution to decrease disease burden.