Wolves and Wigan both agreed fees with Hamilton for McCarthy, but Latics have persuaded the Republic of Ireland Under-21 international to make the switch to the DW Stadium rather than Molineux.
Portsmouth and Celtic had also been linked with the player.
McCarthy, 18, has agreed a four-year deal at Wigan and is expected to tie up the loose ends of the move on Tuesday.
The move is a coup for Latics boss Roberto Martinez, who has been a long-term admirer of McCarthy, with the youngster being chased by a host of clubs.
McCarthy paid tribute to his former Hamilton team-mates after establishing himself as one of the best prospects in Britain at New Douglas Park.
"I had an absolutely brilliant time at Accies," McCarthy told the club's official website.
"The club have been tremendous with me. I made so many good friends and I wish everyone at Accies all the very best."