The south coast side have signed Cork, 19, as a replacement for their captain Andrew Davies who signed for Stoke City earlier in the week.
Cork made 35 appearances for the Iron last season, scoring twice, and could make his debut for the Saints against Derby County on Saturday.
He became an integral part of United's side last season, and believes that exeprience will help him at St Mary's.
"Scunthorpe were a little unlucky to go down and I thought we could have got some results against a few more teams," he told Southampton's official website.
"Hopefully I can fit in well at Southampton because I've got Championship experience. I want to play as many games as I can and want to help Saints do well."