The Latics, who shocked City in last year's final when Ben Watson's stoppage-time goal saw them claim a 1-0 win to lift the trophy, remained on course to defend their crown thanks to their 2-1 win at the Etihad on Sunday.
The Sky Bet Championship side will face a Gunners side bidding to end a nine-year wait for silverwar e.
Hull will play Sheffield United in the other semi-final.
Hull earned their place at Wembley with a 3-0 victory over Sunderland on Sunday to line up an all-Yorkshire clash against Sky Bet League One side Sheffield United.
In beating Charlton 2-0, the Blades became the first club from the third tier to reach the semi-finals of the competition since Wycombe in 2001.
Hull boss Steve Bruce admitted that the draw, which saw his side avoid Arsenal, was favourable but was taking nothing for granted against the Blades.
"It's a great draw," he said.
"Sheffield United have had a wonderful run and they've beaten every team in front of them so it's never going to be easy but you've got to be honest and I'm sure Sheffield United were the same as us - you just want to avoid the big boys.
"When you get to quarter-finals and semi-finals, we haven't been there since 1930. That's a bit of the magic of the Cup.
"The magic of the FA Cup for me will never disappear.
"The magic of it when you get to the big quarter-finals, semi-finals, finals - whether you're a player, manager, coach or supporter you enjoy the occasion."
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