Generally speaking, the symptoms of encephalitis in babies usually start with fever. Encephalitis is an infectious disease, and the majority of cases present with fever, which could be either high or low. Next is vomiting. Since small infants cannot express headache, they usually manifest symptoms through crying, irritability, and restlessness. Additionally, there might be lethargy and malaise. Some may experience seizures, and others might have stiff neck, characterized by rigidity of the neck and changes in muscle tone of the limbs, among other symptoms. These are all symptoms of encephalitis.