Introduction: Allgrove syndrome (Triple A syndrome) is a rare autosomal recessive disorder with classical triad of achalasia, alacrima, and adrenal insufficiency . Although neurological involvement—such as peripheral neuropathy , autonomic dysfunction, and pyramidal involvement, the autoimmune encephalitis has been rarely described in association with this condition. The most frequent and consistent neurological manifestations is cognitive impairment. Case presentation: A 6-year-old boy born to non-consanguineous parents, previously healthy , presented with acute behavioral changes, seizures, and altered sensorium, based on the presence of acute encephalopathy , seizures, supportive neuroimaging, EEG findings, CSF inflammatory changes, and exclusion of infection, a diagnosis of autoimmune encephalitis was made. The child was treated with intravenous immunoglobulin (IVIG) and intravenous methylprednisolone. He showed clinical improvement and was followed up in the pediatric clinic. Subsequently , reported skin hyperpigmentation, including nail and buccal mucosa. On reevaluation, she reiterated the longstanding history of alacrima and swallowing difficulties. Achalasia confirmed on barium swallow , Short Synacthen test confirmed adrenal insufficiency . Hydrocortisone replacement therapy was started, paediatric surgical and ophthalmology follow-up arranged. At 6-month follow-up, there was no recurrence of seizures or encephalitis. However, gradual cognitive decline was noted. Conclusion: Autoimmune encephalitis may represent a rare neurological manifestation of Allgrove syndrome. Ongoing neurodevelopmental monitoring is essential, as cognitive decline may occur despite seizure control and appropriate endocrine management.