The H1N1 virus is one of the highly contagious strains that leads to epidemic influenza every year in winter. In this outbreak sometimes rare complications of this infection occur.  This report presents a rare case of encephalitis caused by H1N1 virus in a 52-year old man. After a day fever and flu like symptoms the patient was admitted in hospital due to decreased level of consciousness. Brain CT was found to be normal and since it was the flu season empiric treatment with vancomycin, ceftriaxone, acyclovir, and Tamiflu was started. In third day of treatment the patient was alert and had no brain dysfunction. CSF samples were positive for H1N1. Staining and culture were negative for CSF and ten lymphocytes were found in CSF samples, also protein and sugar levels were in normal ranges. The patient with encephalopathy associated influenza was treated with Tamiflu within 10 days and he was discharged in good condition. It is noteworthy that influenza can cause loss of consciousness due to encephalitis or meningoencephalitis, especially during influenza season.