The 15-year-old, who has represented Republic of Ireland at Under 17 level, was offered scholarship terms with the League One club this summer having been at the Valley for the past three years.
However, upon United showing a strong interest in his services, he has decided on a switch to the Premier League champions.
Despite the centre-half not officially having a contract with Charlton, the two clubs have come to an agreement which includes additional payments depending on McGinty's success with United.
Charlton chairman Richard Murray told the club's official website: "To have a club like Manchester United tracking our youth players clearly shows the quality that our academy is currently producing.
"Of course, nothing would have made us happier than Sean coming through the ranks and representing our first team, and our coaches had high hopes for him. We did our utmost to persuade him to stay. But equally, joining such a big Premier League club is obviously an attractive prospect, and Sean and his family made it clear that they wanted to move north to United.
"Manchester United have behaved entirely honourably throughout the process and I'd like to thank them for that."