A 9-year-old male with autism and a history of well-controlled epilepsy presented with acute headache, fever, and generalized tonic-clonic seizures. Initial diagnostics, including imaging and cerebrospinal fluid analysis, were inconclusive. However, further serological testing suggested the presence of the chikungunya virus, establishing a diagnosis of chikungunya-associated neurological manifestation. The patient was treated with anticonvulsants, antibiotics for secondary bacterial pneumonia, and supportive care, leading to a gradual recovery. This case highlights the importance of considering systemic viral infections in pediatric patients with neurological symptoms and underscores the potential for arboviruses like chikungunya to cause neurological manifestation.