Stoke boss Pulis upset for Whelan after hamstring setback
He now looks likely to miss two vital upcoming international qualifiers for his country.
"He [Glenn] felt his hamstring again so we had no option than to take him off," Pulis told the club's website. "I'm pretty sure that he won't be off playing with Ireland, which will be a huge disappointment to him, as of course it is to us too.
"He is a massive Ireland supporter and he is a very patriotic lad, so he will be desperate to be out there playing for his country and helping them to get the results they are looking for over the next nine or ten days.
"Unfortunately though, with the injury that he has it looks unlikely that he will be able to play a part in any of their two games."