Background: Epstein-Barr virus (EBV) mononucleosis is rarely associated with central nervous system (CNS) abnormalities, which usually appear later in the course of the illness. Neurological disorders caused by EBV infectious mononucleosis include optic neuritis, transverse myelitis, aseptic meningitis, encephalitis, meningoencephalitis, cranial nerve (CN) palsies, and Guillain-Barré syndrome. Primary EBV infection often leads to elevated liver enzymes and infectious mononucleosis syndrome, but acute symptomatic hepatitis without typical EBV presentations is relatively uncommon. We present the case of a 12-year-old male who presented with fever, lethargy, and unusual behavior for one day, and fever for five days. The physical examination results were normal. Changes in EBV specific antibodies and EBV-PCR were used to diagnose EBV encephalitis when normal examinations revealed symptoms of acute hepatitis.