Ferry, who spent 10 years as coach of the Blackbirds, will replace Ron Everhart, who was fired, Duquesne Athletics Director Greg Amodio announced.
"Ferry has been a winner at every level," Amodio said. "Through a combination of hard work, strong character and outstanding leadership he experienced unprecedented success at LIU."
Ferry will formally be introduced Thursday.
The 44-year-old took the Blackbirds from a 5-22 record in 2002-03 to a 27-6 mark in 2010-11, then guided them to a 25-9 season in 2011-12.
Ferry boasts a 254-168 career record with two NCAA Tournament appearances at the Division I level.
The Dukes, meanwhile, went 16-15 this season, losing to Massachusetts in the first round of the Atlantic 10 Championship.