The Republic of Ireland international, who joined from Sheffield Wednesday in 2008 for £500,000, has become an important player in central midfield having initially struggled to hold down a regular place when the Potters were promoted to the Premier League.
Whelan, 28 on Friday, also has the option for a further year after his new deal expires.
Whelan has had a significant 12 months as he was part of the side which reached the FA Cup final, losing to Manchester City, and also helped the Republic qualify for Euro 2012.
"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,'' he told cfc.com.
"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 12 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.''
Manager Tony Pulis said the midfielder had proven to be an invaluable member of the squad.
"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,'' he said.
"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.''