Anti-N-methyl-D-aspartate-type glutamate receptor autoimmune encephalitis can arise in the setting of ovarian teratoma and often responds to resection. When arising in the absence of tumor failure to respond to treatment may be more likely, and affected patients often require intensive care. To further understanding of mechanisms and potential management we present findings from an autopsy conducted on a young woman who died from refractory autoimmune encephalitis of this type. Rituximab was administered 70 days before death, and both 37 and 14 days before death CD19+ lymphocytes were only 0.1% of blood cells. 10 sessions of plasmapheresis were performed following rituximab treatment. Nonetheless, the auto-antibodies were present in serum 4 days before death, demonstrating ongoing antibody production. The hippocampus and medial temporal lobe demonstrated inflammation with T-cell and prominent microglial involvement, but no plasma cells or plasmablasts were found there, or anywhere in the brain, despite an extensive search. Examination of lymph node tissue identified many plasma cells along sinusoids. These findings demonstrate that the antibody-producing cells are long-lived and likely reside in lymphoid tissue. Awareness of continuing antibody production, the extra-CNS site, the indication for cytotoxic therapy, and the potential for biopsy assessment may lead to more effective treatment.