Autoimmune neurology is a rapidly developing specialty driven by an increasing recognition of autoimmunity as the cause for a broad set of neurologic disorders and ongoing discovery of new neural autoantibodies associated with recognizable clinical syndromes. The diversity of clinical presentations, unique pathophysiology, and the complexity of available treatments requires a dedicated multidisciplinary team to diagnose and manage patients. In this article, we focus on antibody-associated autoimmune encephalitis (AE) to illustrate broader themes applicable to the specialty. We discuss common diagnostic challenges including the utilization of clinical assessment tools along with the determination of the prognostic significance of certain autoantibodies, with a focus on implications for long-term management. A growing body of literature demonstrates the long-term cognitive, behavioral, and physical sequelae of AE. Dedicated resources are needed to effectively manage these patients. These resources may be best provided by experienced neurology clinics in partnership with other neurologic subspecialists, as well as psychiatrists, neuropsychologists, and physical medicine and rehabilitation providers.