The club confirmed that the defender has been retained for next season despite struggling for regular first-team football over the last 12 months.
The 29-year-old made only six appearances in all competitions last season, but he remains part of Potters boss Mark Hughes' plans for the next campaign.
Wilkinson, who made his first-team debut for the club in 2001, is now determined to force his way back into contention for a regular place in the senior side.
"I am very happy to sign again for Stoke. This is a club that I love and I want to stay at," Wilkinson told the club's official website.
"It would be hard for me to leave, so it wasn't a hard decision to make and I am delighted to get the deal done.
"It's been a frustrating season for me, not playing as many games as I would have liked to, but that is a credit to the lads who have played.
"There have not been many chances to be involved but I feel that I still have something to offer, which is why I am happy to stay.
"I need to keep working hard and hopefully my chance will come again."