 In 2004, Flaherty became the offensive line coach of the New York Giants.He was hired to a new staff under new head coach Tom Coughlin, he would remain in this position until 2015 when Tom Coughlin stepped down, thus, a coaching staff overhaul began.On January 22, 2016, Flaherty was hired by new head coach Chip Kelly to become the offensive line coach of the San Francisco 49ers.