Former Manchester United Academy boss Joyce takes over at the DW Stadium after Gary Caldwell was sacked last week having won just two of the Latics opening 14 games.
Joyce has spent the past eight years at Old Trafford managing the Under-21 and Under-23 squads and joins the Lancashire outfit on a three and a half year contract.
The 51-year-old is considered one of the best coaches in the country and has recorded back to back Under 21 Premier League titles among several other trophies and has previously coached current Manchester United first team regulars Paul Pogba, Jesse Lingard and Marcus Rashford.
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He will take charge of training this morning and will be in the DW Stadium dugout for the first time when Wigan face Reading this Saturday, November 5.
Meanwhile, Wolverhampton Wanderers have stepped up their pursuit to find Walter Zenga's replacement with Nigel Pearson reported to have had a second interview with the club.
Italian Zenga was sacked by Wolves after just 87 days at the helm after the former Italy goalkeeper took just four wins from his opening 14 league matches at Molineux.
However, former Derby County boss Pearson is not the only name in the frame - ex-Aston Villa and Norwich City manager Paul Lambert and Tim Sherwood are also believe to be on the shortlist of potential candidates.