There is increasing interest in the role of autoantibodies in acquired autoimmune central nervous system disorders. N-methyl-d-aspartate receptor (NMDAR) encephalitis is an autoimmune encephalitis defined by the presence of autoantibodies that bind to the NMDAR. Although there is evidence of NMDAR antibody pathogenicity, it is unclear which treatment results in the best outcome. We measured the proportion of B-cells in the cerebrospinal fluid of two children with NMDAR encephalitis (a 6-year-old male and a 4-year-old female), one in the acute phase and one in the relapsing phase. The proportion of CD19+ B-cells in both children was greater than 10%, significantly higher than seen in non-inflammatory neurological disorders (<1%). This finding supports the use of drugs, such as rituximab, that deplete B-cells in severe or refractory cases of NMDAR encephalitis, and lends further support to the humoral autoimmune hypothesis in NMDAR encephalitis.