McGinty moved to Old Trafford from Charlton in 2009 and has taken in previous spells with Morecambe, Oxford and Carlisle to earn Under-19 honours with the Republic of Ireland.
Rovers boss Ronnie Moore stated the 19-year-old's versatility made him an appealing recruit.
"I'm really pleased to bring Sean in from Manchester United," said Moore on his club's official website. "He can play left-back or centre-back and gives us extra options in our defence.
"Our chief scout Dave Philpotts has watched him play for United's Under-21s and he's a big, strong lad who likes to get forward.
"Manchester United rate him highly and I'm sure he'll be a good addition to our squad. I'd like to thank Sir Alex Ferguson for allowing Sean to join us."