The Latics have beaten off interest from their Premier League rivals Wolves to land the Republic of Ireland Under-21 international.
McCarthy is believed to have agreed a four-year deal at Wigan and is expected to tie up the loose ends of the move on Tuesday.
"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."