Wigan stunned Man City in last season's final to win the first major trophy in their history, and have again defied the odds this term to reach the last eight.
Having knocked out Cardiff City on Saturday, Whelan admitted he was fully expecting the draw for the sixth round to send them to the Etihad Stadium.
"When they were in the hat and being drawn the one thing I thought is, 'We'll get Manchester City away at their ground' and sure enough out it came," Whelan told Sky Sports News.
"The FA Cup is such a wonderful event with things like this happening. We're facing City again and I'm really, really looking forward to it."
The gloss was taken off Wigan's FA Cup success last season somewhat as they suffered relegation, and the priority this season is again their league campaign.
The Latics are currently ninth in the Championship, seven points adrift of a play-off spot but with at least one game in hand on most of their promotion rivals.
Whelan added: "We've got a very big season. We've been in Europe and we've got to play something like 58 to 60 games this season, and our No.1 objective is obviously to get back in the Premier League.
"If we can get in the play-offs and get back to Wembley, in a different way this time through the play-offs, I've got a slight feeling we might just do it."