The 25-year-old moved to the Britannia Stadium from Sheffield Wednesday for £500,000 in January 2008 and has established himself as a regular in central midfield.
"I'm obviously delighted to have secured my future here with the club," said Whelan.
"I've worked hard since I arrived here and it's great to have been rewarded with a new deal."
Whelan played an important part in the Potters' promotion-winning campaign of 2007/08 but initially struggled to make the breakthrough at Premier League level.
However, he re-established his first-team place in the latter half of last season and hopes to be able to progress now the finalities of his new contract have been signed.
"It's taken a week or two to iron out but I never had to think about it really," he told stokecityfc.com.
"I want to play at the highest level and achieve as much as I can and I feel I can fulfil my ambitions at Stoke. I was obviously disappointed for myself (at the start of last season) because I wanted to show I could play at this level.
"But I kept my head up and worked as hard as I could and fortunately I got my chance and have taken it. I turned things around at the turn of the year but I don't want to get too far ahead of myself because I know I still have a lot to learn.
"Hopefully I can continue improving here under the gaffer (Tony Pulis) and retain my spot in the starting XI. I learned a lot last season and feel better with every game that goes by."