The Potters reached at least the quarter-finals of the cup in 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.
Pulis's team will now attempt to bounce back against a side they have not beaten since May 2009.
Five of the last seven games between the sides have been draws while Wigan have won on the other two occasions.
Pulis said: "The players will be a bit disappointed because we've had some great runs in the FA Cup but we now have to 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.
"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.
After a run of 10 games unbeaten to finish 2012, the Potters have begun 2013 with three consecutive league defeats, shipping 13 goals in four games.
Pulis is likely to make a few changes to the team that faced City, with Asmir Begovic certain to return in goal and Geoff Cameron set to slot back in to the back four.
Pulis said of the American full-back: "I thought it was a good time to give Geoff a rest on Saturday.
"He's been complaining about one or two muscle problems, which is probably down to the fact that he isn't used to the amount of games he's played over the last 12 months."
Pulis will also have Glenn Whelan available after the midfielder escaped punishment for a two-footed tackle on City's Javi Garcia on Saturday.
The Republic of Ireland international has been criticised for the challenge but, because referee Howard Webb saw it but did not take action at the time, Whelan cannot be punished retrospectively.