Seronegative autoimmune encephalitis (AE) is AE without any identifiable pathogenic antibody. Although it is a major subtype of AE, many unmet clinical needs exist in terms of clinical characteristics, treatments, and prognosis. In this institutional cohort study, patients diagnosed with seronegative AE with available 2-year outcomes were analysed for the disease course, 2-year outcome prediction system, effect of immunotherapy, necessity of further immunotherapy at 6 or 12 months, and pattern of brain atrophy. Seronegative AE was subcategorized into antibody-negative probable AE (ANPRA), autoimmune limbic encephalitis (LE), and acute disseminated encephalomyelitis (ADEM). Poor 2-year outcome was defined by modified Rankin scale [mRS] scores 3‒6, and the 2-year serial data of Clinical Assessment Scales in Autoimmune Encephalitis (CASE) score was used for longitudinal data analyses. A total of 147 patients were included. The frequency of achieving a good 2-year outcome (mRS 0‒2) was 56.5%. The ANPRA subtype exhibited the poorest outcomes, although the baseline severity was similar among the subtypes. The RAPID score, consisting of five early utilizable clinical factors, refractory status epilepticus, age of onset ≥ 60 years, probable AE (ANPRA subtype), infratentorial involvement, and delay of immunotherapy ≥ 1 month, was associated with poorer 2-year outcomes. Any immunotherapy was associated with clinical improvement in the patients with low risk for poor 2-year outcomes (RAPID scores 0–1), and the combination immunotherapy of steroid, immunoglobulin, rituximab, and tocilizumab was associated with better outcomes in the patients with high risk for poor 2-year outcomes (RAPID scores 2-5). In patients with persistent disease at 6 months, continuing immunotherapy was associated with more improvement, while the effect of continuing immunotherapy for more than 12 months was unclear. In the longitudinal analysis of MRI, the development of cerebellar atrophy indicated poor outcomes, while the absence of diffuse cerebral atrophy or medial temporal atrophy indicated the possibility of a good outcome. This study provides information about the clinical characteristics and courses, the effect of immunotherapy and its duration, and prognostic factors in seronegative AE.