Anti-GQ1b antibody syndrome, including Miller Fisher syndrome, Guillain-Barré syndrome with ophthalmoplegia, Bickerstaff’s brainstem encephalitis, and acute ophthalmoplegia without ataxia, has overlapped clinical symptoms and mostly associated with anti-GQ1b immunoglobulin (Ig) G antibody. We report two cases of anti-GQ1b antibody syndrome mainly presenting with a severe headache. The 60-year-old man was admitted for severe headache and gait disturbance. Neurological examination revealed limb and truncal ataxia, areflexia, nystagmus, and ophthalmoplegia. Serum IgG anti-GQ1b antibody was positive. He recovered after intravenous (IV) immunoglobulin and steroid. The 23-year-old man suffered from severe headache (visual analogue scale=10) within the periorbital area. Ophthalmoplegia with gaze-evoked nystagmus were revealed. Serum IgG anti-GQ1b and anti-GT1a antibodies were positive. Headache was improved by IV immunoglobulin and steroid. The pathophysiology of headache in anti-GQ1b antibody syndrome is largely unknown. The affected nerve or structures in the brainstem including the trigeminovascular system may induce intractable severe headache.