Logan, 23 has started three matches for the Premier League side Manchester Cityand has also enjoyed loan spells with Grimsby Town and Stockport County in the last two seasons as well as the Iron.
Logan made four Championship appearances for Scunthorpe - the Iron lost three and drew one - after joining on loan in November 2007.
The Tranmere manager John Barnes hopes he will help tighten his side's backline after securing a season-long loan.
"I'm delighted to be able to bring Shaleum to Tranmere for the season. He's a talented young player who will improve our defence," he said.
"I'd like to thank Manchester City manager Mark Hughes for allowing Shaleum to join us on loan."