McAllister signed for the Iron from Cowdenbeath in July 2013, making 89 appearances for the club.
The 28-year-old has also had spells with Sheffield Wednesday, Bury, Mansfield, Shrewsbury and Port Vale.
McAllister is the second former Iron player to join Grimsby this summer, following the signing of Andrew Boyce.
Find all the latest football transfers on our dedicated page.
League Two side Grimsby Town have signed midfielder Sean McAllister on a two-year deal following his release by League One Scunthorpe United.