Objectives To determine the incidence and clinical relevance of neuronal autoantibodies in children with demyelinating syndromes. Methods We conducted a prospective study including 31 consecutive children with demyelinating syndromes. Four patients with N-Methyl- D -aspartate receptor (NMDAR) encephalitis, 32 patients with Guillain-Barre syndrome, 13 children with benign childhood epilepsy, and 28 healthy children were used as controls. Prior to initiating immunomodulatory therapy, serum samples were tested for antibodies against NMDAR, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) 1, AMPAR2, leucine-rich glioma-activated protein 1, contactin-associated protein 2, gamma-aminobutyric acid B receptors, paraneoplastic ma antigen 2 (PNMA2/Ta), Yo, Ri, Hu, CV2, amphiphysin, and aquaporin-4 by indirect immunofluorescence assays. Results Three anti-neuronal antibodies were detected; NMDAR antibody in one with multiple sclerosis, PNMA2/Ta antibody in one with multiple sclerosis, and Yo antibody in one with clinically isolated syndrome. The positivity rate of neuronal autoantibodies in demyelinating syndrome was 10%. All seropositive patients were found to be negative for tumor screening. None of these patients exhibited symptoms of encephalitis. Conclusion Children with demyelinating syndromes without symptoms of encephalitis can be positive for anti-neuronal antibodies.