Flaherty began his coaching career at his alma mater, Delone Catholic High School in McSherrystown, Pennsylvania from 1978–79.
Flaherty moved to the collegiate ranks, coaching the offensive line at his alma mater, East Stroudsburg University, from 1980–81.
At Penn State, he helped the Nittany Lions win the 1982 National Championship with a Sugar Bowl victory over Georgia.
He was hired to a new staff under new head coach Tom Coughlin, and received two Super Bowl rings during this time.
[2] On July 29, 2019, the Dolphins head coach, Brian Flores, fired Flaherty just four days into training camp and replaced him with team analyst Dave DeGuglielmo.