The new deal will keep the 27-year-old Republic of Ireland midfielder with the Potters until the summer of 2016.
“Glenn has played a big part in our achievements since he came to the club and it is important to look after players who have been the bedrock of that success,” said manager Tony Pulis.
“He has had a fantastic time these past 12 months, and he’s shown that he’s a player who thrives on being challenged to step up to the next level.
“That’s probably the Celtic blood in him and a steely determination to prove people wrong, which has included even myself on occasions.”
“I am loving life at the moment and things are going really well, so I am absolutely delighted to commit my long term future to the club,” Whelan said.
“We have enjoyed a remarkable past few years with everything that we have achieved and I believe that even more success can be achieved in the future.
“I am very excited about what the next few years could have in store, and I am proud to be a part of it as we look to continue the club’s excellent progress.
“All of the hard work I have done over the past twelve months has paid off. To play at Wembley twice, reach the FA Cup final, play in Europe and be doing well at international level has certainly made it a memorable time for me.”
