Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is an autoimmune disease mediated by IgG1 or IgG3 antibodies to the GluN1 subunit of the NMDAR, resulting in downregulation of NMDARs. Early diagnosis, prompt reduction of anti-NMDAR antibodies, and removal of associated ovarian tumors when identified are important drivers of prognosis. Immunohistochemical studies were carried out to evaluate B cell, plasma cell, and T-cell infiltrates in the brain of a 3-year-old patient with anti-NMDAR encephalitis who failed to show improvement after plasma exchange and Rituximab treatment. Complement activation was evaluated by C4d staining. Plasma cells and B-cells were rarely detected in the brain. In contrast, persistent intraparenchymal infiltrates and perivascular CD3+ T cells and evidence of complement activation were detected. Activated microglia and microglial nodules were also detected in the frontal lobes and the basal ganglia. The role of T cells and complement activation should be investigated in patients who do not respond to plasma exchange and Rituximab treatment.