The 2022 Highly Pathogenic Avian Influenza (HPAI) outbreak that occurred in 2022 in many European countries affected several seabird species. Among them, Northern gannets (Morus bassanus), were particularly impacted. We conducted aerial surveys in waters around the two largest gannet colonies in Ireland (Little Skellig and Bull Rock, together representing 87% of the national population) in September 2022. During surveys, 184 dead gannets were recorded on survey effort, representing 3.74% of the total number of gannets recorded. We estimated the abundance of dead gannets in the surveyed area at 1,526 (95% CIs 1,299–1,793) individuals. The percentage of dead gannets observed was used to estimate a minimum local population mortality of 3,118 individuals across both colonies. Aerial surveys proved a reliable methodology providing key information on gannet mortality derived from HPAI at sea. The study provides the first estimate of gannet mortality in the two largest gannetries in Ireland.