We report on the changing epidemiology of two important flaviviruses in Nepal: Japanese encephalitis (JE) and dengue viruses. Morbidity and mortality in Nepal is in the thousands since JE was introduced in 1978. Nepal launched an extensive laboratory-based JE surveillance in 2004. Nepal experienced a remarkable reduction in disease burden after mass immunizations from 2005 to 2010, when 2,040 JE infections and 205 JE-related deaths were confirmed. With its emergence in 2006, dengue has become a significant challenge in the country, highlighted by a sudden outbreak in 2010 that resulted in 359 confirmed dengue infections. Currently, both viruses cocirculate in Nepal. Here, we document the remarkable expansion of dengue in Nepal, which urgently requires national surveillance to refine the burden and make recommendations regarding control and prevention programs. We believe that the use of existing JE surveillance network for integrated dengue surveillance may represent the most appropriate alternative.