De Bohun will join the FFA after seven years in charge of game and market development at CA to start his second stint with the A-League, having held the position of operations manager from 2004 until 2005.
De Bohun replaces Lyall Gorman who vacated the role to take up his post as executive chairman of new A-League club the Western Sydney Wanderers.
FFA chief executive Ben Buckley said he is thrilled to have lured de Bohun back to the A-League.
"Damien has a wonderful mix of senior executive experience in the sports industry and a life-long passion for football," Buckley said in a statement.
"I'm delighted to have secured a high-calibre executive in Damien. I know he has the right skills, energy and football administration knowledge to implement our goals for a stable and sustainable A-League."
De Bohun, whose first foray into football administration was as chief executive of Football Federation Victoria in 2003, said he's excited by the challenge.
"Football has always been a big part of my life as a player, coach and referee," he said.
"But it's the professional challenge of managing the A-League that has me most excited about the new role.
"I think the current structure of the A-League provides a very solid foundation to build on the growth in attendances, TV audiences and memberships last season and I can't wait to get started."
De Bohun will begin his new role in early August.