Whelan sustained the injury during the Republic of Ireland's 1-1 draw with Germany in Gelsenkirchen on October 14, forcing him off after 54 minutes of the Euro 2016 qualifier.
The 30-year-old subsequently missed Stoke's 2-1 victory over Swansea on Saturday, and is now unlikely to return until early December.
It means Whelan will also miss Ireland's group game with Scotland on November 14, along with a number of Stoke fixtures.
City manager Mark Hughes said: "He got a kick on the outside of his leg, and there is a slight fracture there.
"He's not been put into a plaster cast
We're going to try and manage it without that because Glenn feels he'll get back sooner.
"But the likelihood is he's going to be out for four to six weeks I'd imagine, which is a blow for Glenn obviously because he is a big part of what we're doing, and we'll miss him.
"He's been playing really well of late, but we'll get him back as soon as we can.
"As for Ireland, knowing Glenn he'll try and make himself available, but my feeling is the game will be too soon for him.
"You have to let nature take it course
With fractures you have to give them enough time to heal."
Source : PA
Source: PA