A DNA vaccine is a plasmid encoding a vaccine antigen together with an efficient eukaryotic promoter to drive protein expression. The chief problem of DNA vaccines has been their suboptimal immunogenicity in humans. Many different flaviviruses infect and cause serious illness and even death in humans, but human vaccines are not available against most of the relevant flaviviruses with the exception of Japanese encephalitis virus. DNA vaccines are easy and fast to produce at relatively low cost, do not require handling of dangerous pathogens, are stable at room temperature allowing for low-cost storage and transportation, and are highly versatile, allowing for rapid changes in coding sequence design and synthesis. This makes a DNA vaccine approach ideally suited for development as a broad-based flavivirus vaccine platform. However, to be useful as a flavivirus prophylactic vaccine platform in humans, a method would need to be found to enhance DNA vaccine immunogenicity without the need for the cumbersome and expensive equipment involved with electroporation. We describe here a protocol used to test different adjuvants with flavivirus DNA vaccines to determine an optimal formulation. An optimal regimen involving a DNA adjuvanted vaccine prime followed by an adjuvanted protein vaccine boost is described and can be applied by readers to solve barriers to the development of other DNA vaccines where immunogenicity is a problem.