Dengue virus (DENV) and Japanese encephalitis virus (JEV) are closely related mosquito-borne flaviviruses. Together, they caused most arthropod-borne diseases in the world. Previously, we had demonstrated that both live attenuated and inactivated JE vaccines elicited cross-protection against DENV infection, and a DNA vaccine candidate expressing JEV prM-E protein (named pCAG-JME) could provide effective protection against JEV infection in mice. In this study, we examined whether the same pCAG-JME could elicit cross-protection against DENV infection. Our results showed that pCAG-JME indeed induced cross-reactive antibodies and cross-protection against four different serotypes of DENV in mice. Interestingly, pCAG-JME-immunized mice also generated both Th1 and Th2 responses when stimulated by all four different serotypes of DENV antigens. Moreover, cross-primed CD8(+) T cell response was also detected following the stimulation of DENV proteins using intracellular cytokine staining. In addition, sera from pCAG-JME-immunized mice significantly reduced the mortality caused by DENV2 infection in severe combination immunodeficiency mouse. These results suggest that both JE and DENV cross-reactive antibodies and cross-primed T cells might play important roles in the cross-protection. The findings of this study also indicate a possibility of developing novel multivalent genetically engineered vaccines against both JEV and DENV.