An outbreak of H3N8 Equine Influenza virus (EIV) that occurred in vaccinated horses in Japan was caused by a genetically divergent EIV isolate of the Florida clade 1 sub-lineage. This virus subsequently entered Australia where it infected thousands of immunologically naïve horses. The objective of this study was to evaluate the ability of a non-updated whole inactivated equine influenza (EI) vaccine to protect if used in the face of an outbreak induced by a virus similar to the ones circulating in Japan and Australia in 2007. Seven naïve Welsh mountain ponies were immunised twice with the commercially available vaccine Duvaxyn IE-T Plus and experimentally infected with A/eq2/Sydney/2888-8/07. Five ponies remained unvaccinated as controls. The ponies were challenged in an ACDP (Advisory Committee on Dangerous Pathogens) Category III containment facility by exposure to a nebulised aerosol of A/eq2/Sydney/2888-8/07 two weeks after the second vaccination. Clinical signs and virus shedding were monitored for 14 days post-challenge infection. After challenge infection, all control ponies developed clinical signs of disease with coughing being particularly noteworthy when compared with vaccinated ponies. Only 3 out of 5 controls developed pyrexia for up to 3 days, and 1 out of 7 vaccinates was pyretic for 1 day. Nasal discharge was evident in both control and vaccinated ponies with no significant difference between groups. Three different methods were used to measure virus shedding in nasal secretions (i.e. titration in embryonated hens' eggs, EIV NP ELISA and EIV NP qRT-PCR). The intensity and duration of EIV shedding significantly decreased in the vaccinated group when compared with the control ponies. All control ponies seroconverted after experimental infection with A/eq2/Sydney/2888-8/07 whereas only 1 out of 7 vaccinated ponies had a significant increase in antibody. Duvaxyn IE-T Plus therefore reduced clinical signs and virus shedding when ponies were challenged with A/eq2/Sydney/2888-8/07 (H3N8), 2 weeks after a second dose of vaccine.