Vaccination by intramuscular injection of naked DNA is very efficient in mouse model, but immunogenicity of DNA vaccines needs to be improved in human use. Thus, we wanted to determine whether suitable electric pulses-mediated DNA delivery technology and DNA prime-protein boost regimen could improve the immunogenicity and protective efficacy of the replicon DNA vaccine pSCARSHc in mouse model. In this study, the immunogenicity and protective efficacy of the replicon DNA vaccine pSCARSHc following electric pulses were dramatically improved in Balb/c mice. Also, priming of the immune response by DNA vaccination followed by a single booster with AHc protein immunogen resulted in very high levels of ELISA and neutralization antibodies and afforded more efficient protection against botulinum neurotoxin serotype A. Therefore, these methods described here potentially provide suitable strategies in developing an efficacious vaccine against Clostridium botulinum neurotoxin serotype A.