Mitchell, an Academy member striving to be drafted, died when he was 16 in a car accident in 2002. He was a part of the Academy's fifth intake.
At the end of each Academy program, each player in the level two squad is assigned a team value, such as courage, commitment, trust and leadership, and vote on which teammate best embodies that trait.
Duggan won the most votes to be named this year's recipient on Monday, at the 2013/2014 squad's final meeting together.
"For me to be voted in by my peers is a huge honour," the Western Jets prospect said.
"It's a humbling award to win among a great bunch of blokes. When we went on the European tour (in April this year) we had a booklet and the medal was highlighted, with Ben's unfortunate story.
"It’s a big honour to have won the medal."
Academy captain, West Australian Brad Walsh, was second placed, with injured Victorian Jake Lever third.
Essendon's Joe Daniher received the medal in 2012, while last year's was shared between Greater Western Sydney's No.2 pick Josh Kelly and Sydney Swans midfielder Lloyd Perris.
Duggan has had a consistent NAB AFL Under-18 Championships for Vic Metro, playing mainly through the midfield.
His balance, left-foot disposal and smarts around the ball make him a highly rated draftee, with the Mitchell Medal confirming his quality off-field character.
"I haven't been outstanding through the championships but I think I've played my role within the team and have done my bit," he said.