The efficacy of different vaccination schedules was evaluated in 17-day-old Pekin ducks using an experimental inactivated whole virus vaccine based on the H5N9 A/chicken/Italy/22A/98 isolate (H5N9-It) and/or a fowlpox recombinant (vFP-H5) expressing a synthetic HA gene from an Asian H5N1 isolate (A/chicken/Indonesia/7/2003). Full protection against clinical signs and shedding was induced by the different vaccination schemes. However, the broadest antibody response and the lowest antibody increase after challenge were observed in the group of ducks whose immune system was primed with the fowlpox vectored vaccine and boosted with the inactivated vaccine, suggesting that this prime-boost strategy induced optimal immunity against H5N1 and minimal viral replication after challenge in ducks. In addition, this prime-boost vaccination scheme was shown to be immunogenic in 1-day-old ducklings.