We assessed the validity of immunoblotting, immunohistochemistry (IHC), and immunocytochemistry (ICC) to detect anti-neuronal antibodies in an attempt to establish a diagnostic approach for pediatric autoimmune encephalitis. Both IHC and ICC had higher sensitivity than immunoblotting and could differentiate between antibodies directed towards intracellular and cell surface antigens. There was a significant correlation between the IHC and ICC results. When patients were divided into encephalitis and non-encephalitis groups, there was no difference in the positivity rate and staining pattern of IHC and ICC between them. In conclusion, IHC and ICC are useful methods to screen for anti-neuronal antibodies. A combination of IHC, ICC, and specific cell-based assays is expected to be an efficient approach for the diagnosis of autoantibody-mediated encephalitis.