Dengue is widespread throughout the tropics globally in more than hundred countries and coincides with various climatic factors for co-infection with other flaviviral infections of the central nervous system (CNS). Dengue and Japanese encephalitis virus co-infection are highly prevalent, with diagnosis dilemma including significant mortality and morbidity in Southeast Asia. Both dengue and Japanese encephalitis transmissions intensify during the rainy season, during which the vector population increases. CNS involvement during dengue and Japanese encephalitis co-infectionassociated acute encephalitis syndrome (AES) is still poorly understood, and therefore, there is a desperate need to understand the etiology, therapeutics, clinical management, and prevention of these tropically neglected diseases. AES can be differentiated from other etiologies of encephalopathy through considering its essential features: sudden onset of fever, cerebrospinal fluid (CSF) comprising inflammatory cells, magnetic resonance imaging (MRI)-based confirmation, and presence of pathogen or pathogenspecific antibodies. Complementary and alternative medicine is progressively being used globally and can be effective for the overall management of this co-infection.2 virus (YFV) [3]. More than half of the global population is now at the risk of getting flavivirus infections where the majority of areas are endemic for more than one flaviviruses which results in the phenomenon of co-infection [4]. The worldwide incident of dengue has extensively grown in few decades [5]. Majority of the dengue cases are asymptomatic, and therefore, it is hard to anticipate the accurate burden of the disease. The rise in number of cases from 2.2 million in the year 2010 to 3.34 million cases in 2016 suggests the sharp increase in the disease burden. The 2016 year is characterized as the largest outbreak for dengue where 2.38 million cases were reported from the region of the Americas where 1.5 million cases were contributed by Brazil alone. Currently 3.9 billion in 128 countries people are at risk of DENV infection [6]. Unlike dengue, Japanese encephalitis (JE) is confined to Southeast Asia and Western Pacific regions. Approximately 68,000 clinical cases of JE are reported annually with 13,000 to 24,000 deaths. Currently more than 3 billion in 24 countries are at risk of JEV infection [7]. The epidemiology of dengue and JE has been depicted in Figure 1.DENV and JEV belongs to the Flaviviridae family, which consists of more than 70 viruses, comprising of single-stranded positive-sense RNA genome protected by envelope protein [8]. Viruses from this family belong to the genus Flavivirus, which are transmitted by mosquitoes or ticks and are characterized as arthropod-borne infections. The transmission cycle of Flavivirus involves animals including human which are considered to be the dead-end hosts [9]. Hematophagous mosquitoes are the transmission vector for these diseases. Aedes albopictus and Aedes aegypti mosquitoes are known to transmit the dengue virus, whereas...