Whelan, who began his career at City, picked up the injury during the Republic of Ireland's 2-1 defeat against Sweden on Friday and assistant boss Mark Bowen admits he is touch and go.
The full extent of the damage has yet to be revealed but the player is undergoing treatment back at the Britannia Stadium in the hope he will be passed fit to face big-spending City.
"It's too early to rate his chances for Saturday, but he is obviously a doubt at this stage of the week," Bowen revealed.
Potters boss Mark Hughes will now be hoping and praying the rest of his international brigade come through the final round of matches unscathed ahead of the weekend.
Stoke last week