Despite the Iron rebuffing two Doncaster bids in recent weeks and Paul Dickov suggesting he'd look elsewhere, Duffy's move to Doncaster is imminent.
Iron chairman Peter Swann told the Scunthorpe Telegraph: "I believe he has already held some form of talks with the club and so it was just about an agreement being reached between the two clubs.
"I'm pleased it's all sorted. Really we just needed to find some common ground between the two clubs.
"We felt their offers were too low, they felt our valuation was too high but we didn't want to stop him moving on and we've worked as hard as we can to get it sorted and get a fair deal for the club.
"It wasn't really a bid as such, more just a conversation between myself and John Ryan (the Doncaster chairman).
"Moving to Doncaster was what Mark wanted and so we did what we could to make it happen."
Callum Kennedy is also close to the Glanford Park exit, with a move to another League Two side in the pipeline.