Background: Acute hepatitis caused by viral organisms which are typically implicated in the cases of encephalitis are rarely reported in literature. The presentation of enteroviral meningoencephalitis predominated with the clinical picture of hepatitis has rarely been recorded in populations other than neonates. Case Presentation: A male 2-year-old, presenting with a fever of 38 to 40 °C with chills and rigors, lethargy and drowsiness for 6 days. Along with the nausea, vomiting and watery diarrhea, he developed mouth ulcers (peri-oral vesicles) during the stay at the hospital. After extensive workup he was later diagnosed with meningoencephalitis and acute hepatitis due to Coxsackie virus A. After a stay of more than a month he was successfully treated and discharge. Conclusion: A more thorough evaluation should be carried out for atypical viral infections presenting with clinical presentation of hepatitis and meningoencephalitis.