DNA vaccination is an effective means of eliciting both humoral and cellular immunity. Most of influenza vaccines targeted at hemagglutinin (HA) show efficient immunogenicity for protecting subjects against influenza virus infection. However, major antigenic variations of HA may facilitate the virus in developing resistance against such vaccines. DNA vaccines encoding conserved antigens protect animals against diverse viral subtypes, but their potency requires further improvement. In the present study, a DNA vaccine encoding the conserved nucleoprotein (NP) with a tissue plasminogen activator (tPA) signal sequence (ptPAs/NP) was generated, and immune responses were examined in vaccinated mice. A higher level of NP expression and secretion was observed in lysates and supernatants of the cells transfected with ptPAs/NP when compared to a plasmid encoding the wild-type full-length NP (pflNP). Immunofluorescence studies showed the cytoplasmic localization of the NP protein expressed from ptPAs/NP, but not from pflNP. In mice, the ptPAs/NP vaccine elicited higher levels of the NP-specific IgG and CD8(+) T cell-stimulating responses than that of pflNP. Vaccination with ptPAs/NP efficiently cleared the homologous H5N1 influenza virus in the infected lungs and induced partial cross-protection against heterologous, highly pathogenic H5N1 strains in mice. Our results may contribute to the development of protective immunity against diverse, highly pathogenic H5N1 virus subtypes.