Objective: To assess the inpatient hospitalization burden and costs of patients with autoimmune encephalitis (AE) at a tertiary care institution. Methods: Adult inpatients with AE were identified retrospectively from July 1, 2005 – June 30, 2015. Demographic and clinical data were collected and analyzed. Billing data were compared to that of patients with herpes simplex encephalitis (HSE). Charges were adjusted for inflation. Results: Of 244 admissions for encephalitis reviewed, 63 patients met criteria for probable or definite AE. Thirty-one (49%) patients were antibody-positive, and twenty-seven (43%) were admitted to the intensive care unit (ICU). Median hospital charges per AE patient were over $70k, median length of stay (LOS) was 15 days, and in hospital mortality was 6%. ICU patients had substantially higher median hospital charges (ICU $173k/ admission vs. non-ICU $50k/ admission, p<0.001). LOS was strongly associated with charges and was driven by delay in diagnosis of AE, prolonged treatment courses, and lack of response to therapy. In comparison with HSE, median hospital charges per AE patient were nearly 4 times higher, median AE LOS was 3 times higher, and total charges over the study period were nearly twice as high. Conclusions: AE patients utilized more inpatient healthcare resources per patient during a ten-year period than HSE at our institution. ICU-admitted AE patients were responsible for a substantially higher financial burden than non-ICU-admitted AE patients. Our data underscore the need for the development of novel diagnostic and therapeutic modalities to improve patient outcomes and decrease hospital burden in AE.