Harley retired in 2009 following 197 games and two flags with Geelong. He also played one match with Port Adelaide.
He then joined AFL NSW/ACT, moving through the ranks to become its general manager, before stepping down at the end of 2013 to focus on his young family, his work with Channel 7 and to further his education.
The 36-year-old has now decided to take on the important role at the Swans, replacing Dean Moore, whose association with the club dates back more than 30 years.
"Tom is a highly regarded person who comes to us with great football experience," Swans chief executive Andrew Ireland said in a statement.
"He was part of a great club in Geelong throughout a very successful era and was one of the most respected leaders in the game.
"We have worked closely together while he was at AFL NSW/ACT and I think he is a great appointment to what is a very challenging role."
Moore served as the club's team manager in the late 1970s, helping to manage its move from South Melbourne to Sydney.
He then moved on to the Victoria Football League before returning at the end of 2009 to replace Ireland in the Swans' football manager's role.
In the statement, Swans coach John Longmire paid tribute to Moore's support and work ethic.
Moore, who will stay involved with the club on a part-time basis, felt it was the right time to move on.
"This is something that has been in the planning for some time," he said.
"And while it is disappointing to bow out after [the Grand Final defeat to Hawthorn], I have thoroughly enjoyed my time in the role.
"I love this club and it has been an enormous privilege to be part of the football department."
