In a repeat of the 2013 FA Cup final, the Blues will look to avenge a shock 1-0 win for the Latics.
Ben Watson famously headed home a stoppage time winner for Wigan in what proved to be Roberto Mancini's last game in charge of City.
And one year later, the Latics jinx struck again as Uwe Rosler returned to guide his Wigan side to a 2-1 win at the Etihad Stadium as the Championship side pulled off another shock win.
That tie came just days after the Blues had secured the Capital One Cup with a 3-1 win over Sunderland - and the Blues have again reached the final of the Carabao Cup final this season.
Wigan, managed by Paul Cook, are two points clear of Shrewsbury Town at the top of League One.
They have already beaten Premier League opposition in the shape of Bournemouth and West Ham in previous rounds.
As well as the 2013 and 2014 clashes, City also faced Wigan in the FA Cup third round in January 1971, with Colin Bell on target in a 1-0 victory.
Ticket details and the exact date of the tie will be announced in the coming days.