RATIONALE: Anti-dipeptidyl-peptidase-like-protein 6 (DPPX) encephalitis is a rare form of autoimmune encephalitis, with no more than 80 cases reported to date. Cases of anti-DPPX encephalitis comorbid malignancy are exceedingly rare. Limited cases and diverse clinical presentations bring difficulties in the understanding of this disease, including the etiology, diagnosis, treatment, and prognosis. Herein, we report a case of insidious-onset anti-DPPX encephalitis in a patient with a prior history of Epstein-Barr Virus (EBV) meningitis diagnosed with gastric cancer after 2 years of follow-up. PATIENT CONCERNS: A 72-year-old emaciated male presented with recurrent seizures over the last 20 years, personality changes over 10 years, and memory loss lasting 2 years. DIAGNOSES: The patient was diagnosed with epilepsy, psychiatric symptoms (agitation and irritability), and mild cognitive impairment. Anti-DPPX encephalitis and prior EBV infection were ultimately diagnosed based on the combination of his symptoms and positive DPPX antibody in serum (titer 1:10) and positive EBV-IgG antibody in cerebrospinal fluid. INTERVENTIONS: The patient received a course of intravenous methylprednisolone and oral sodium valproate to treat the seizures. OUTCOMES: After 10 days of treatment, no seizures reoccurred, although the psychiatric symptoms persisted, and his serum antibody against DPPX was still positive (titer 1:10). Unfortunately, the family members asked for the patient to be discharged automatically and refused oral steroids after discharge. Through regular telephone follow-ups for 2 years after discharge, we learned that the patient did not experience any similar convulsions but still showed irritability when administered perphenazine. Unfortunately, the patient had gastric cancer with multiple metastases and was receiving palliative care. LESSONS: This report illustrates a rare case of EBV meningitis in childhood, resulting in a long-standing, stable course of anti-DPPX encephalitis, and subsequent gastric cancer. This case broadens the atypical presentation spectrum of anti-DPPX encephalitis and emphasizes the need for screening for malignant tumors, including lymphoma, nasopharyngeal carcinoma, and gastric cancer, particularly in patients with latent EBV infection.