Equine influenza virus (EIV) is a major cause of respiratory disease in horses. Vaccination is an effective tool for infection control. Although various EIV vaccines are widely available, major outbreaks occurred in Europe in 2018 involving a new EIV H3N8 FC1 strain. In France, it was reported that both unvaccinated and vaccinated horses were affected despite >80% vaccination coverage and most horses being vaccinated with a vaccine expressing FC1 antigen. This study assessed whether vaccine type, next to antigenic difference between vaccine and field strain, plays a role. Horses were vaccinated with an ISCOMatrix-adjuvanted, whole inactivated virus vaccine (Equilis Prequenza) and experimentally infected with the new FC1 outbreak strain. Serology (HI), clinical signs, and virus shedding were evaluated in vaccinated compared to unvaccinated horses. Results showed a significant reduction in clinical signs and a lack of virus shedding in vaccinated horses compared to unvaccinated controls. From these results, it can be concluded that Equilis Prequenza provides a high level of protection to challenge with the new FC1 outbreak strain. This suggests that, apart from antigenic differences between vaccine and field strain, other aspects of the vaccine may also play an important role in determining field efficacy.