Low pathogenic influenza viruses of H6 hemagglutinin (HA) subtype have a high prevalence among aquatic and domestic birds and have caused outbreaks in poultry worldwide. The first human infection with wild avian influenza H6N1 virus was reported in Taiwan and these subtype viruses may continue to evolve and accumulate changes which increasing the potential risk of human-to-human transmission. To develop a vaccine against influenza viruses of the H6 subtype, we displayed the HA gene on the baculovirus surface (Bac-HA), and studied its vaccine efficacy against a lethal challenge with mouse-adapted RG-H6(Shorebird) virus carrying the H6 HA gene from A/shorebird/DE/12/2004 (H6N8) virus and 7 genes from A/Puerto Rico/8/1934 (H1N1) virus. Immunization with 256 HA units of Bac-HA via the intranasal route triggered HA-specific serum and mucosal antibodies in mice besides increased HA inhibition titers compared to mice immunized subcutaneously. Moreover, we observed an increase in cellular immune response (IL-4) and improved in vitro neutralization activity in the mice immunized intranasally with live Bac-HA compared to mice immunized with inactivated influenza virus (IV). Interestingly, Bac-HA intranasal immunized mice showed one fold higher neutralization titer against heterologous H6 influenza virus compared to inactivated IV immunized mice. In addition, the live Bac-HA, administered through either immunization route, as well as the adjuvanted inactivated Bac-HA, administered subcutaneously, conferred 100% protection to mice challenged with homologous mouse-adapted RG-H6(Shorebird) virus. The reduction in viral titers and extend of histopathological changes of Bac-HA immunized mice lungs further demonstrated the protective efficacy of Bac-HA. Hence, the recombinant baculovirus subunit vaccine is an alternative candidate against H6 subtypes that could be propagated and administered with minimal biosafety concerns.