A 33-year-old woman presented with stabbing perianal pain and intermittent headache and photophobia. Examination revealed atypical multiple perianal fissures with non-specific neurological findings. Polymerase chain reaction of the perianal swab and cerebrospinal fluid examination confirmed the diagnosis of perianal herpes simplex type 2 ulcer with herpes meningitis. This report emphasizes the importance of performing further investigations on patients with atypical anal fissures with or without systemic symptoms and signs to avoid misdiagnosis, inappropriate treatment and prolonged discomfort.