In 1977 he became the head basketball coach and accounting teacher of his high school alma mater, Malvern Prep.

He left La Salle to become head coach Tom Schneider's top assistant at Penn in 1988.

Dunphy's 310 wins are the most by any Penn coach and are second all-time in the Ivy League to Princeton's Pete Carril.

They lost a close game to Michigan State (who advanced to the Sweet Sixteen) in the first round of the 2008 NCAA tournament.

Dunphy's 2009–10 Temple team won 11 of its first 13 games, including a victory over cross-town rival and then-third ranked Villanova, before falling to top-ranked Kansas.

The 2009–10 team also ranked in the top twenty-five for more than eleven straight weeks in both major polls, and won its third consecutive Atlantic 10 tournament title.

However, for the third straight season, Dunphy's Owls lost in the first round of NCAA tournament, this time to Ivy League champion Cornell.

Dunphy would lead the Owls back to the tournament in the 2011–12 season, only to be upset in the second round by South Florida 58–44.

In the following season after losing senior guards Juan Fernandez and Ramone Moore, Dunphy led the Owls to an early-season upset of then 3-seed Syracuse – a team that eventually made the Final Four – at Madison Square Garden and #21 VCU on the final day of the regular season to secure a 6th straight NCAA tournament appearance.

The Owls would knock off 8-seed North Carolina State 76–72 in the second round before losing to 1-seed Indiana 58–52 in a game that Temple led the majority of the way.

On April 5, 2022, The Philadelphia Inquirer reported that the La Salle would hire Dunphy to be the Explorers' next men's basketball coach.

Dunphy, who lived his first 10 years in Southwest Philadelphia before moving to nearby Drexel Hill, starred at La Salle from 1967 through 1970.

He served as a co-captain his senior year when he averaged 18.6 ppg and led the team in assists, while also being named the MVP of the annual Quaker City Basketball Tournament.