The Potters reached at least the quarter-finals of the cup in all of the last three seasons, with the highlight being their run to the final in 2011.
Manchester City denied Stoke the silverware on that occasion and it was Roberto Mancini's side who knocked them out in the fourth round on Saturday, 1-0 again the scoreline.
It was a disappointing result for Pulis and his team, and they will now attempt to bounce back against a side they have not beaten since their first season in the Barclays Premier League, in May 2009.
Five of the last seven games between the sides have been draws while Wigan have won on the other two occasions, including at the Britannia Stadium on the final day of the 2010/11 season to avoid relegation.
Pulis told the club's official website: "The players will be a bit disappointed because we've had some great runs in the FA Cup but we now have get back on track in the league.
"We need everyone's help and we need to be focused because the Premier League is so important to us and we want to get to 40 points as quickly as we can.
"We certainly need our supporters behind us for what will be a tough game. They're a good side who have been something of a bogey team for us. We've played well for long periods in games against them but not got what we deserved in terms of results."
Wigan again find themselves fighting for top-flight survival and have won only once in the last 10 games but Stoke, too, are in need of a victory.