Objective: The main objective is to assess the challenges in diagnosis and treatment while managing seronegative cases of autoimmune encephalitis (AIE) in Indian children. Methods: A cohort study of patients with AIE was done where clinical presentations, investigations, management were analyzed and these patients were followed up to assess the evolution of the disease. Results: Nine patients were included in the study. Four patients presented with super-refractory status epilepticus (SRSE). Other presentations were behavioral change, hemiplegia, and autonomic dysfunction. Initial magnetic resonance imaging brain was suggestive of AIE in two patients. Only two were seropositive for cerebrospinal fluid (CSF) autoimmune panel. Five patients responded to the first-line immunotherapy and four required the second-line immunotherapy. Conclusion: The possibility of autoimmune encephalitis should be considered in patients with super-refractory status epilepticus. A large proportion of children with suspected AE may be “seronegative.” A trial of immunotherapy should be given to these children when there is a strong clinical suspicion of autoimmune encephalitis even in the absence of cerebrospinal fluid autoantibodies.