The 29-year-old is the club's longest-serving current player, having made his debut in 2001, and has put pen to paper on a new contract at the Britannia Stadium.
Wilkinson, who was limited to just six appearances this season, has also agreed an option for a further 12 months as part of the deal.
Despite only using the versatile defender sparingly in his debut season at the club, Mark Hughes backed Wilkinson to regain a place in the side.
"Everyone knows how much the club means to Andy – he's Stoke City through and through," Hughes told Stoke's official website.
"He didn't play as many games last season as he would have hoped but he's determined to force his way back into the side on a regular basis and still has a part to play going forward."
The club's chief executive Tony Scholes added: "Andy has given the club fantastic service and was a key figure in our promotion from the Championship and helping us to become established in the Premier League.
"We're delighted we have been able to reach an agreement with him over a new contract."
