Diagnosing autoimmune encephalitis relies on clinical, radiological, and serological studies. Several autoantibodies have been implicated and recognized, with dozens of potential targets identified in the past 20 years. Despite that progress, some patients with encephalitis present a diagnostic dilemma with a seronegative status. The presence of other autoimmune diseases in a patient with encephalitis should provide a clue to the autoimmune nature of a developing neurological syndrome (cognitive, psychiatric, behavioral, and catatonia). In this report, we describe the case of a young man with type 1 diabetes mellitus who was diagnosed with seronegative autoimmune encephalitis after presenting with catatonia. We describe the lengthy clinical course, the various therapeutic trials, and his clinical outcome and response to B-cell depleting agent. This study also discusses the potential pathophysiologic pathways, providing a rationale for the diagnostic workup and therapeutic options for autoimmune encephalopathy in this case presentation.