Japanese encephalitis (JE) and malaria would coexist in the areas where both illnesses are endemic with overlapping clinical pictures, especially in a case of febrile encephalopathy with hepatosplenomegaly. However, there are no published data till date showing concurrent infection of these two agents despite both diseases being coendemic in many areas. We report a case of concurrent infection of JE and mixed plasmodium infection, where the case, initially diagnosed as cerebral malaria did not improve on antimalarials and alternative diagnosis of JEV encephalitis was thought which was confirmed by a serological test. To the best of our knowledge, this is the first case report of concurrent Japanese encephalitis with mixed plasmodium infection. We report a case of 3-year-old male child, who presented with febrile encephalopathy with hepatosplenomegaly. Based on a rapid diagnostic test and peripheral smear examination, a diagnosis of mixed P.Vivax and P.falciparum infection was made and the patient was treated with quinine and doxycycline. However, besides giving antimalarials the patient did not improve and an alternative diagnosis of JE was considered as the patient was from the endemic zone of Japanese encephalitis. Cerebrospinal fluid (CSF) of the patient was sent for a virological study which came out to be positive for JE IgM in CSF, which is confirmatory of JE infection. In a patient with febrile encephalopathy with hepatosplenomegaly especially in areas coendemic for JE and malaria, the possibility of mixed infection should be kept in mind.