 On January 14, 2017, Flaherty was hired by new head coach Doug Marrone to become the offensive line coach of the Jacksonville Jaguars.On December 31, 2018 following a disappointing 5-11 campaign, Flaherty was one of three assistant coaches that were fired at the end of the season.On February 8, 2019, the Miami Dolphins announced they had hired Flaherty as their offensive line coach.