Mortimer was a member of the 2004 and 2006 Mayo teams, both of which lost to Kerry in the All-Ireland Final. In 2006, Mortimer was the top scorer in the All-Ireland Senior Football Championship (1-32) as Mayo took the Connacht title, came from behind to beat Dublin in the semi-final but were ultimately thrashed by Kerry in the 2006 All-Ireland Senior Football Championship Final. Rewarding his great year, Mortimer was selected in the 2006 GAA Football All Stars and the GPA Gaelic Team of the Year.