Ryan moved to Glanford Park in the summer. He was out-of-contract at the Crown Ground, but as he was under the age of 24 the Lancashire side were entitled to a transfer fee.
The Iron must pay £55,000 immediately followed by payments of £27,500 in October and January.
There are £15,000 payments once he reaches 15, 30, 45 and 60 first-team appearances and £25,000 if the Iron secure promotion to the Championship this season or next.
There is also a 20 per cent sell-on clause of any profit on any future sale of the player.
"The good thing is that the fee has now been set and the two clubs and the player can move on," said the Iron general manager David Beeby.
Beeby attended the Manchester hearing, along with manager Alan Knill, chairman Steve Wharton and the player.
"We would have liked to have received more, but I'm sure Scunthorpe would have wanted to pay less," said Stanley chief executive Rob Heys.
"Jimmy is a good player who served us well and we wish him and everyone at
Scunthorpe all the best for the future."