Ben Watson scored a late winner as the DW Stadium outfit claimed a shock Wembley victory to win the trophy on that occasion in May and Wigan have already knocked out two Premier League opponents in this season's tournament.
Elsewhere, Liverpool will face neighbours Everton if they beat Arsenal on Sunday, while Sheffield United and Sheffield Wednesday will meet each other if they get past Nottingham Forest and Charlton Athletic respectively.
In the remaining last eight tie, Brighton and Hove Albion or Hull City, who meet on Monday, will host Sunderland.
The ties will be played on the weekend of March 8/9.
The draw in full:
Arsenal or Liverpool v Everton
Brighton and Hove Albion or Hull City v Sunderland
Sheffield United or Nottingham Forest v Sheffield Wednesday or Charlton Athletic
Manchester City v Wigan Athletic
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