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We reported a 43-year-old male patient who presented with headache and diplopia. The cerebrospinal fluid analysis showed pleocytosis, suggesting acute meningitis. The subsequent polymerase chain reaction and genetic sequencing of blood and cerebrospinal fluid showed that the causative organism was Anaplasma phagocytophilum. This case suggests that we should consider anaplasmosis as a causative agent of acute meningitis; if an unexplained meningitis patient shows no response to any treatments.